# # Amber Ubuntu Installation Output File # For more information, see http://www.somewhereville.com/?p=345 # Damian Allis, damian@somewhereville.com, www.somewhereville.com # mkdir /opt/amber10/bin /opt/amber10/lib /opt/amber10/include mkdir: cannot create directory `/opt/amber10/bin': File exists mkdir: cannot create directory `/opt/amber10/lib': File exists mkdir: cannot create directory `/opt/amber10/include': File exists make: [install] Error 1 (ignored) (cd ucpp-1.3 && make install ) make[1]: Entering directory `/opt/amber10/src/ucpp-1.3' Makefile:35: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' gcc -c -m64 -DBINTRAJ -DSTAND_ALONE mem.c gcc -c -m64 -DBINTRAJ -DSTAND_ALONE nhash.c gcc -c -m64 -DBINTRAJ -DSTAND_ALONE cpp.c gcc -c -m64 -DBINTRAJ -DSTAND_ALONE lexer.c gcc -c -m64 -DBINTRAJ -DSTAND_ALONE assert.c gcc -c -m64 -DBINTRAJ -DSTAND_ALONE macro.c gcc -c -m64 -DBINTRAJ -DSTAND_ALONE eval.c gcc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o mv ucpp /opt/amber10/bin make[1]: Leaving directory `/opt/amber10/src/ucpp-1.3' (cd byacc && make install ) make[1]: Entering directory `/opt/amber10/src/byacc' gcc -c -m64 -DBINTRAJ -o closure.o closure.c gcc -c -m64 -DBINTRAJ -o error.o error.c gcc -c -m64 -DBINTRAJ -o lalr.o lalr.c gcc -c -m64 -DBINTRAJ -o lr0.o lr0.c gcc -c -m64 -DBINTRAJ -o main.o main.c gcc -c -m64 -DBINTRAJ -o mkpar.o mkpar.c gcc -c -m64 -DBINTRAJ -o output.o output.c gcc -c -m64 -DBINTRAJ -o reader.o reader.c gcc -c -m64 -DBINTRAJ -o skeleton.o skeleton.c gcc -c -m64 -DBINTRAJ -o symtab.o symtab.c gcc -c -m64 -DBINTRAJ -o verbose.o verbose.c gcc -c -m64 -DBINTRAJ -o warshall.o warshall.c main.o: In function `create_file_names': main.c:(.text+0x645): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' mv yacc /opt/amber10/bin make[1]: Leaving directory `/opt/amber10/src/byacc' (cd carpack && make install ); make[1]: Entering directory `/opt/amber10/src/carpack' Makefile:7: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' gcc -c -O3 -m64 -DBINTRAJ -o dgetv0.o dgetv0.c gcc -c -O3 -m64 -DBINTRAJ -o dlaqrb.o dlaqrb.c gcc -c -O3 -m64 -DBINTRAJ -o dnaitr.o dnaitr.c gcc -c -O3 -m64 -DBINTRAJ -o dnapps.o dnapps.c gcc -c -O3 -m64 -DBINTRAJ -o dnaup2.o dnaup2.c gcc -c -O3 -m64 -DBINTRAJ -o dnaupd.o dnaupd.c gcc -c -O3 -m64 -DBINTRAJ -o dnconv.o dnconv.c gcc -c -O3 -m64 -DBINTRAJ -o dneigh.o dneigh.c gcc -c -O3 -m64 -DBINTRAJ -o dneupd.o dneupd.c gcc -c -O3 -m64 -DBINTRAJ -o dngets.o dngets.c gcc -c -O3 -m64 -DBINTRAJ -o dsaitr.o dsaitr.c gcc -c -O3 -m64 -DBINTRAJ -o dsapps.o dsapps.c gcc -c -O3 -m64 -DBINTRAJ -o dsaup2.o dsaup2.c gcc -c -O3 -m64 -DBINTRAJ -o dsaupd.o dsaupd.c gcc -c -O3 -m64 -DBINTRAJ -o dsconv.o dsconv.c gcc -c -O3 -m64 -DBINTRAJ -o dseigt.o dseigt.c gcc -c -O3 -m64 -DBINTRAJ -o dsesrt.o dsesrt.c gcc -c -O3 -m64 -DBINTRAJ -o dseupd.o dseupd.c gcc -c -O3 -m64 -DBINTRAJ -o dsgets.o dsgets.c gcc -c -O3 -m64 -DBINTRAJ -o dsortc.o dsortc.c gcc -c -O3 -m64 -DBINTRAJ -o dsortr.o dsortr.c gcc -c -O3 -m64 -DBINTRAJ -o dstatn.o dstatn.c gcc -c -O3 -m64 -DBINTRAJ -o dstats.o dstats.c gcc -c -O3 -m64 -DBINTRAJ -o dstqrb.o dstqrb.c gcc -c -O3 -m64 -DBINTRAJ -o dsarpack.o dsarpack.c gcc -c -O3 -m64 -DBINTRAJ -o wallclock.o wallclock.c gcc -c -O3 -m64 -DBINTRAJ -o dmout.o dmout.c gcc -c -O3 -m64 -DBINTRAJ -o ivout.o ivout.c gcc -c -O3 -m64 -DBINTRAJ -o dvout.o dvout.c ar rv arpack.a dgetv0.o dlaqrb.o dnaitr.o dnapps.o dnaup2.o dnaupd.o dnconv.o dneigh.o dneupd.o dngets.o dsaitr.o dsapps.o dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o dsortr.o dstatn.o dstats.o dstqrb.o dsarpack.o wallclock.o dmout.o ivout.o dvout.o ar: creating arpack.a a - dgetv0.o a - dlaqrb.o a - dnaitr.o a - dnapps.o a - dnaup2.o a - dnaupd.o a - dnconv.o a - dneigh.o a - dneupd.o a - dngets.o a - dsaitr.o a - dsapps.o a - dsaup2.o a - dsaupd.o a - dsconv.o a - dseigt.o a - dsesrt.o a - dseupd.o a - dsgets.o a - dsortc.o a - dsortr.o a - dstatn.o a - dstats.o a - dstqrb.o a - dsarpack.o a - wallclock.o a - dmout.o a - ivout.o a - dvout.o ranlib arpack.a mv arpack.a /opt/amber10/lib make[1]: Leaving directory `/opt/amber10/src/carpack' (cd clapack && make install ) make[1]: Entering directory `/opt/amber10/src/clapack' Makefile:7: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' gcc -c -O3 -m64 -DBINTRAJ -o dsyev.o dsyev.c gcc -c -O3 -m64 -DBINTRAJ -o dsyevd.o dsyevd.c gcc -c -O3 -m64 -DBINTRAJ -o dormtr.o dormtr.c gcc -c -O3 -m64 -DBINTRAJ -o dormql.o dormql.c gcc -c -O3 -m64 -DBINTRAJ -o dormqr.o dormqr.c gcc -c -O3 -m64 -DBINTRAJ -o dlansy.o dlansy.c gcc -c -O3 -m64 -DBINTRAJ -o dsytrd.o dsytrd.c gcc -c -O3 -m64 -DBINTRAJ -o dorgtr.o dorgtr.c gcc -c -O3 -m64 -DBINTRAJ -o dsteqr.o dsteqr.c gcc -c -O3 -m64 -DBINTRAJ -o dsterf.o dsterf.c gcc -c -O3 -m64 -DBINTRAJ -o dlascl.o dlascl.c gcc -c -O0 -o dlamch.o dlamch.c gcc -c -O3 -m64 -DBINTRAJ -o ilaenv.o ilaenv.c gcc -c -O3 -m64 -DBINTRAJ -o dlassq.o dlassq.c gcc -c -O3 -m64 -DBINTRAJ -o dsytd2.o dsytd2.c gcc -c -O3 -m64 -DBINTRAJ -o dorm2l.o dorm2l.c gcc -c -O3 -m64 -DBINTRAJ -o dlatrd.o dlatrd.c gcc -c -O3 -m64 -DBINTRAJ -o dorgql.o dorgql.c gcc -c -O3 -m64 -DBINTRAJ -o dorgqr.o dorgqr.c gcc -c -O3 -m64 -DBINTRAJ -o dlasrt.o dlasrt.c gcc -c -O3 -m64 -DBINTRAJ -o dlaset.o dlaset.c gcc -c -O3 -m64 -DBINTRAJ -o dlanst.o dlanst.c gcc -c -O3 -m64 -DBINTRAJ -o dlaev2.o dlaev2.c gcc -c -O3 -m64 -DBINTRAJ -o dlasr.o dlasr.c gcc -c -O3 -m64 -DBINTRAJ -o dlapy2.o dlapy2.c gcc -c -O3 -m64 -DBINTRAJ -o dlartg.o dlartg.c gcc -c -O3 -m64 -DBINTRAJ -o dlae2.o dlae2.c gcc -c -O3 -m64 -DBINTRAJ -o dorg2r.o dorg2r.c gcc -c -O3 -m64 -DBINTRAJ -o dlarft.o dlarft.c gcc -c -O3 -m64 -DBINTRAJ -o dlarfb.o dlarfb.c gcc -c -O3 -m64 -DBINTRAJ -o dorg2l.o dorg2l.c gcc -c -O3 -m64 -DBINTRAJ -o dlarfg.o dlarfg.c gcc -c -O3 -m64 -DBINTRAJ -o dlarf.o dlarf.c gcc -c -O3 -m64 -DBINTRAJ -o dspev.o dspev.c gcc -c -O3 -m64 -DBINTRAJ -o dlansp.o dlansp.c gcc -c -O3 -m64 -DBINTRAJ -o dsptrd.o dsptrd.c gcc -c -O3 -m64 -DBINTRAJ -o dopgtr.o dopgtr.c gcc -c -O3 -m64 -DBINTRAJ -o dposv.o dposv.c gcc -c -O3 -m64 -DBINTRAJ -o dppsv.o dppsv.c gcc -c -O3 -m64 -DBINTRAJ -o dspsv.o dspsv.c gcc -c -O3 -m64 -DBINTRAJ -o dgeev.o dgeev.c gcc -c -O3 -m64 -DBINTRAJ -o dsptrs.o dsptrs.c gcc -c -O3 -m64 -DBINTRAJ -o dsptrf.o dsptrf.c gcc -c -O3 -m64 -DBINTRAJ -o dpptrs.o dpptrs.c gcc -c -O3 -m64 -DBINTRAJ -o dpptrf.o dpptrf.c gcc -c -O3 -m64 -DBINTRAJ -o dgebak.o dgebak.c gcc -c -O3 -m64 -DBINTRAJ -o dtrevc.o dtrevc.c gcc -c -O3 -m64 -DBINTRAJ -o dlacpy.o dlacpy.c gcc -c -O3 -m64 -DBINTRAJ -o dhseqr.o dhseqr.c gcc -c -O3 -m64 -DBINTRAJ -o dorghr.o dorghr.c gcc -c -O3 -m64 -DBINTRAJ -o dgehrd.o dgehrd.c gcc -c -O3 -m64 -DBINTRAJ -o dgebal.o dgebal.c gcc -c -O3 -m64 -DBINTRAJ -o dlange.o dlange.c gcc -c -O3 -m64 -DBINTRAJ -o dlabad.o dlabad.c gcc -c -O3 -m64 -DBINTRAJ -o dlahqr.o dlahqr.c gcc -c -O3 -m64 -DBINTRAJ -o dlarfx.o dlarfx.c gcc -c -O3 -m64 -DBINTRAJ -o dlanhs.o dlanhs.c gcc -c -O3 -m64 -DBINTRAJ -o dlaln2.o dlaln2.c gcc -c -O3 -m64 -DBINTRAJ -o dgehd2.o dgehd2.c gcc -c -O3 -m64 -DBINTRAJ -o dlahrd.o dlahrd.c gcc -c -O3 -m64 -DBINTRAJ -o dlanv2.o dlanv2.c gcc -c -O3 -m64 -DBINTRAJ -o dladiv.o dladiv.c gcc -c -O3 -m64 -DBINTRAJ -o dgerq2.o dgerq2.c gcc -c -O3 -m64 -DBINTRAJ -o dorm2r.o dorm2r.c gcc -c -O3 -m64 -DBINTRAJ -o dlarnv.o dlarnv.c gcc -c -O3 -m64 -DBINTRAJ -o dgeqr2.o dgeqr2.c gcc -c -O3 -m64 -DBINTRAJ -o dlaruv.o dlaruv.c gcc -c -O3 -m64 -DBINTRAJ -o dspevd.o dspevd.c gcc -c -O3 -m64 -DBINTRAJ -o dstedc.o dstedc.c gcc -c -O3 -m64 -DBINTRAJ -o dopmtr.o dopmtr.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed0.o dlaed0.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed1.o dlaed1.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed7.o dlaed7.c gcc -c -O3 -m64 -DBINTRAJ -o dlaeda.o dlaeda.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed8.o dlaed8.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed9.o dlaed9.c gcc -c -O3 -m64 -DBINTRAJ -o dlamrg.o dlamrg.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed2.o dlaed2.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed3.o dlaed3.c gcc -c -O3 -m64 -DBINTRAJ -o dsygv.o dsygv.c gcc -c -O3 -m64 -DBINTRAJ -o dsygst.o dsygst.c gcc -c -O3 -m64 -DBINTRAJ -o dsygs2.o dsygs2.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed4.o dlaed4.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed5.o dlaed5.c gcc -c -O3 -m64 -DBINTRAJ -o dlaed6.o dlaed6.c gcc -c -O3 -m64 -DBINTRAJ -o dpotrf.o dpotrf.c gcc -c -O3 -m64 -DBINTRAJ -o dpotrs.o dpotrs.c gcc -c -O3 -m64 -DBINTRAJ -o dpotf2.o dpotf2.c gcc -c -O3 -m64 -DBINTRAJ -o ieeeck.o ieeeck.c ar rv lapack.a dsyev.o dsyevd.o dormtr.o dormql.o dormqr.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o dlascl.o dlamch.o ilaenv.o dlassq.o dsytd2.o dorm2l.o dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o dopgtr.o dposv.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o dlaed3.o dsygv.o dsygst.o dsygs2.o dlaed4.o dlaed5.o dlaed6.o dpotrf.o dpotrs.o dpotf2.o ieeeck.o dsyevd.o dormtr.o dormqr.o dormql.o dorm2l.o ar: creating lapack.a a - dsyev.o a - dsyevd.o a - dormtr.o a - dormql.o a - dormqr.o a - dlansy.o a - dsytrd.o a - dorgtr.o a - dsteqr.o a - dsterf.o a - dlascl.o a - dlamch.o a - ilaenv.o a - dlassq.o a - dsytd2.o a - dorm2l.o a - dlatrd.o a - dorgql.o a - dorgqr.o a - dlasrt.o a - dlaset.o a - dlanst.o a - dlaev2.o a - dlasr.o a - dlapy2.o a - dlartg.o a - dlae2.o a - dorg2r.o a - dlarft.o a - dlarfb.o a - dorg2l.o a - dlarfg.o a - dlarf.o a - dspev.o a - dlansp.o a - dsptrd.o a - dopgtr.o a - dposv.o a - dppsv.o a - dspsv.o a - dgeev.o a - dsptrs.o a - dsptrf.o a - dpptrs.o a - dpptrf.o a - dgebak.o a - dtrevc.o a - dlacpy.o a - dhseqr.o a - dorghr.o a - dgehrd.o a - dgebal.o a - dlange.o a - dlabad.o a - dlahqr.o a - dlarfx.o a - dlanhs.o a - dlaln2.o a - dgehd2.o a - dlahrd.o a - dlanv2.o a - dladiv.o a - dgerq2.o a - dorm2r.o a - dlarnv.o a - dgeqr2.o a - dlaruv.o a - dspevd.o a - dstedc.o a - dopmtr.o a - dlaed0.o a - dlaed1.o a - dlaed7.o a - dlaeda.o a - dlaed8.o a - dlaed9.o a - dlamrg.o a - dlaed2.o a - dlaed3.o a - dsygv.o a - dsygst.o a - dsygs2.o a - dlaed4.o a - dlaed5.o a - dlaed6.o a - dpotrf.o a - dpotrs.o a - dpotf2.o a - ieeeck.o a - dsyevd.o a - dormtr.o a - dormqr.o a - dormql.o a - dorm2l.o ranlib lapack.a mv lapack.a /opt/amber10/lib make[1]: Leaving directory `/opt/amber10/src/clapack' (cd cblas && make install ) make[1]: Entering directory `/opt/amber10/src/cblas' Makefile:7: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' gcc -c -O3 -m64 -DBINTRAJ -o dasum.o dasum.c gcc -c -O3 -m64 -DBINTRAJ -o daxpy.o daxpy.c gcc -c -O3 -m64 -DBINTRAJ -o dcopy.o dcopy.c gcc -c -O3 -m64 -DBINTRAJ -o ddot.o ddot.c gcc -c -O3 -m64 -DBINTRAJ -o dgbmv.o dgbmv.c gcc -c -O3 -m64 -DBINTRAJ -o dgemm.o dgemm.c gcc -c -O3 -m64 -DBINTRAJ -o dgemv.o dgemv.c gcc -c -O3 -m64 -DBINTRAJ -o dger.o dger.c gcc -c -O3 -m64 -DBINTRAJ -o dnrm2.o dnrm2.c gcc -c -O3 -m64 -DBINTRAJ -o drot.o drot.c gcc -c -O3 -m64 -DBINTRAJ -o drotg.o drotg.c gcc -c -O3 -m64 -DBINTRAJ -o dsbmv.o dsbmv.c gcc -c -O3 -m64 -DBINTRAJ -o dscal.o dscal.c gcc -c -O3 -m64 -DBINTRAJ -o dspmv.o dspmv.c gcc -c -O3 -m64 -DBINTRAJ -o dspr.o dspr.c gcc -c -O3 -m64 -DBINTRAJ -o dspr2.o dspr2.c gcc -c -O3 -m64 -DBINTRAJ -o dswap.o dswap.c gcc -c -O3 -m64 -DBINTRAJ -o dsymm.o dsymm.c gcc -c -O3 -m64 -DBINTRAJ -o dsymv.o dsymv.c gcc -c -O3 -m64 -DBINTRAJ -o dsyr.o dsyr.c gcc -c -O3 -m64 -DBINTRAJ -o dsyr2.o dsyr2.c gcc -c -O3 -m64 -DBINTRAJ -o dsyr2k.o dsyr2k.c gcc -c -O3 -m64 -DBINTRAJ -o dsyrk.o dsyrk.c gcc -c -O3 -m64 -DBINTRAJ -o dtbmv.o dtbmv.c gcc -c -O3 -m64 -DBINTRAJ -o dtbsv.o dtbsv.c gcc -c -O3 -m64 -DBINTRAJ -o dtpmv.o dtpmv.c gcc -c -O3 -m64 -DBINTRAJ -o dtpsv.o dtpsv.c gcc -c -O3 -m64 -DBINTRAJ -o dtrmm.o dtrmm.c gcc -c -O3 -m64 -DBINTRAJ -o dtrmv.o dtrmv.c gcc -c -O3 -m64 -DBINTRAJ -o dtrsm.o dtrsm.c gcc -c -O3 -m64 -DBINTRAJ -o dtrsv.o dtrsv.c gcc -c -O3 -m64 -DBINTRAJ -o idamax.o idamax.c gcc -c -O3 -m64 -DBINTRAJ -o lsame.o lsame.c gcc -c -O3 -m64 -DBINTRAJ -o xerbla.o xerbla.c ar rv blas.a dasum.o daxpy.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o idamax.o lsame.o xerbla.o ar: creating blas.a a - dasum.o a - daxpy.o a - dcopy.o a - ddot.o a - dgbmv.o a - dgemm.o a - dgemv.o a - dger.o a - dnrm2.o a - drot.o a - drotg.o a - dsbmv.o a - dscal.o a - dspmv.o a - dspr.o a - dspr2.o a - dswap.o a - dsymm.o a - dsymv.o a - dsyr.o a - dsyr2.o a - dsyr2k.o a - dsyrk.o a - dtbmv.o a - dtbsv.o a - dtpmv.o a - dtpsv.o a - dtrmm.o a - dtrmv.o a - dtrsm.o a - dtrsv.o a - idamax.o a - lsame.o a - xerbla.o ranlib blas.a mv blas.a /opt/amber10/lib make[1]: Leaving directory `/opt/amber10/src/cblas' (cd f2c && make install ) make[1]: Entering directory `/opt/amber10/src/f2c' Makefile:7: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' gcc -c -O3 -m64 -DBINTRAJ -o abort_.o abort_.c gcc -c -O3 -m64 -DBINTRAJ -o d_atan.o d_atan.c gcc -c -O3 -m64 -DBINTRAJ -o d_cosh.o d_cosh.c gcc -c -O3 -m64 -DBINTRAJ -o d_int.o d_int.c gcc -c -O3 -m64 -DBINTRAJ -o d_nint.o d_nint.c gcc -c -O3 -m64 -DBINTRAJ -o d_sinh.o d_sinh.c gcc -c -O3 -m64 -DBINTRAJ -o d_abs.o d_abs.c gcc -c -O3 -m64 -DBINTRAJ -o d_atn2.o d_atn2.c gcc -c -O3 -m64 -DBINTRAJ -o d_dim.o d_dim.c gcc -c -O3 -m64 -DBINTRAJ -o d_lg10.o d_lg10.c gcc -c -O3 -m64 -DBINTRAJ -o d_prod.o d_prod.c gcc -c -O3 -m64 -DBINTRAJ -o d_sqrt.o d_sqrt.c gcc -c -O3 -m64 -DBINTRAJ -o exit_.o exit_.c gcc -c -O3 -m64 -DBINTRAJ -o d_acos.o d_acos.c gcc -c -O3 -m64 -DBINTRAJ -o d_exp.o d_exp.c gcc -c -O3 -m64 -DBINTRAJ -o d_log.o d_log.c gcc -c -O3 -m64 -DBINTRAJ -o d_sign.o d_sign.c gcc -c -O3 -m64 -DBINTRAJ -o d_tan.o d_tan.c gcc -c -O3 -m64 -DBINTRAJ -o d_asin.o d_asin.c gcc -c -O3 -m64 -DBINTRAJ -o d_cos.o d_cos.c gcc -c -O3 -m64 -DBINTRAJ -o d_mod.o d_mod.c gcc -c -O3 -m64 -DBINTRAJ -o d_sin.o d_sin.c gcc -c -O3 -m64 -DBINTRAJ -o d_tanh.o d_tanh.c gcc -c -O3 -m64 -DBINTRAJ -o wsfe.o wsfe.c gcc -c -O3 -m64 -DBINTRAJ -o s_cmp.o s_cmp.c gcc -c -O3 -m64 -DBINTRAJ -o s_copy.o s_copy.c gcc -c -O3 -m64 -DBINTRAJ -o s_paus.o s_paus.c gcc -c -O3 -m64 -DBINTRAJ -o s_rnge.o s_rnge.c gcc -c -O3 -m64 -DBINTRAJ -o s_stop.o s_stop.c gcc -c -O3 -m64 -DBINTRAJ -o wsle.o wsle.c gcc -c -O3 -m64 -DBINTRAJ -o xwsne.o xwsne.c gcc -c -O3 -m64 -DBINTRAJ -o util.o util.c gcc -c -O3 -m64 -DBINTRAJ -o wref.o wref.c gcc -c -O3 -m64 -DBINTRAJ -o wrtfmt.o wrtfmt.c gcc -c -O3 -m64 -DBINTRAJ -o rsne.o rsne.c gcc -c -O3 -m64 -DBINTRAJ -o sfe.o sfe.c gcc -c -O3 -m64 -DBINTRAJ -o sue.o sue.c gcc -c -O3 -m64 -DBINTRAJ -o uio.o uio.c gcc -c -O3 -m64 -DBINTRAJ -o open.o open.c gcc -c -O3 -m64 -DBINTRAJ -o rdfmt.o rdfmt.c gcc -c -O3 -m64 -DBINTRAJ -o rewind.o rewind.c gcc -c -O3 -m64 -DBINTRAJ -o rsfe.o rsfe.c gcc -c -O3 -m64 -DBINTRAJ -o rsli.o rsli.c gcc -c -O3 -m64 -DBINTRAJ -o ilnw.o ilnw.c gcc -c -O3 -m64 -DBINTRAJ -o inquire.o inquire.c gcc -c -O3 -m64 -DBINTRAJ -o lread.o lread.c gcc -c -O3 -m64 -DBINTRAJ -o fmtlib.o fmtlib.c gcc -c -O3 -m64 -DBINTRAJ -o ftell_.o ftell_.c gcc -c -O3 -m64 -DBINTRAJ -o iio.o iio.c gcc -c -O3 -m64 -DBINTRAJ -o err.o err.c gcc -c -O3 -m64 -DBINTRAJ -o close.o close.c gcc -c -O3 -m64 -DBINTRAJ -o dfe.o dfe.c gcc -c -O3 -m64 -DBINTRAJ -o dolio.o dolio.c gcc -c -O3 -m64 -DBINTRAJ -o due.o due.c gcc -c -O3 -m64 -DBINTRAJ -o endfile.o endfile.c gcc -c -O3 -m64 -DBINTRAJ -o backspace.o backspace.c gcc -c -O3 -m64 -DBINTRAJ -o fmt.o fmt.c gcc -c -O3 -m64 -DBINTRAJ -o sig_die.o sig_die.c gcc -c -O3 -m64 -DBINTRAJ -o pow_dd.o pow_dd.c gcc -c -O3 -m64 -DBINTRAJ -o pow_di.o pow_di.c gcc -c -O3 -m64 -DBINTRAJ -o pow_ii.o pow_ii.c gcc -c -O3 -m64 -DBINTRAJ -o lwrite.o lwrite.c gcc -c -O3 -m64 -DBINTRAJ -o i_len.o i_len.c gcc -c -O3 -m64 -DBINTRAJ -o s_cat.o s_cat.c gcc -c -O3 -m64 -DBINTRAJ -o F77_aloc.o F77_aloc.c gcc -c -O3 -m64 -DBINTRAJ -o wsne.o wsne.c gcc -c -O3 -m64 -DBINTRAJ -o typesize.o typesize.c ar rv f2c.a abort_.o d_atan.o d_cosh.o d_int.o d_nint.o d_sinh.o d_abs.o d_atn2.o d_dim.o d_lg10.o d_prod.o d_sqrt.o exit_.o d_acos.o d_exp.o d_log.o d_sign.o d_tan.o d_asin.o d_cos.o d_mod.o d_sin.o d_tanh.o wsfe.o s_cmp.o s_copy.o s_paus.o s_rnge.o s_stop.o wsle.o xwsne.o util.o wref.o wrtfmt.o rsne.o sfe.o sue.o uio.o open.o rdfmt.o rewind.o rsfe.o rsli.o ilnw.o inquire.o lread.o fmtlib.o ftell_.o iio.o err.o close.o dfe.o dolio.o due.o endfile.o backspace.o fmt.o sig_die.o pow_dd.o pow_di.o pow_ii.o lwrite.o i_len.o s_cat.o F77_aloc.o wsne.o typesize.o ar: creating f2c.a a - abort_.o a - d_atan.o a - d_cosh.o a - d_int.o a - d_nint.o a - d_sinh.o a - d_abs.o a - d_atn2.o a - d_dim.o a - d_lg10.o a - d_prod.o a - d_sqrt.o a - exit_.o a - d_acos.o a - d_exp.o a - d_log.o a - d_sign.o a - d_tan.o a - d_asin.o a - d_cos.o a - d_mod.o a - d_sin.o a - d_tanh.o a - wsfe.o a - s_cmp.o a - s_copy.o a - s_paus.o a - s_rnge.o a - s_stop.o a - wsle.o a - xwsne.o a - util.o a - wref.o a - wrtfmt.o a - rsne.o a - sfe.o a - sue.o a - uio.o a - open.o a - rdfmt.o a - rewind.o a - rsfe.o a - rsli.o a - ilnw.o a - inquire.o a - lread.o a - fmtlib.o a - ftell_.o a - iio.o a - err.o a - close.o a - dfe.o a - dolio.o a - due.o a - endfile.o a - backspace.o a - fmt.o a - sig_die.o a - pow_dd.o a - pow_di.o a - pow_ii.o a - lwrite.o a - i_len.o a - s_cat.o a - F77_aloc.o a - wsne.o a - typesize.o ranlib f2c.a mv f2c.a /opt/amber10/lib make[1]: Leaving directory `/opt/amber10/src/f2c' (cd c9x-complex && make skip ) make[1]: Entering directory `/opt/amber10/src/c9x-complex' using built-in (C99) complex.h functionality make[1]: Leaving directory `/opt/amber10/src/c9x-complex' (cd cifparse && make install ) make[1]: Entering directory `/opt/amber10/src/cifparse' Makefile:7: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' flex -t cifparse.l | sed 's/yy/cifp/g' > lex.cif.c /opt/amber10/bin/yacc -v -d cifparse.y sed 's/yy/cifp/g' < y.tab.c > cifp.tab.c sed 's/yy/cifp/g' < y.tab.h > cifp.tab.h rm y.tab.c y.tab.h gcc -c -m64 -DBINTRAJ lex.cif.c cifparse.l: In function ‘delete_punctuation’: cifparse.l:274: warning: assignment makes integer from pointer without a cast gcc -c -m64 -DBINTRAJ -Dflex cifp.tab.c gcc -c -m64 -DBINTRAJ cifparse.c cifparse.c: In function ‘ndb_cif_write_category’: cifparse.c:287: warning: cast from pointer to integer of different size cifparse.c: In function ‘ndb_cif_print_formatted_item_value’: cifparse.c:370: warning: cast from pointer to integer of different size cifparse.c:388: warning: cast from pointer to integer of different size cifparse.c: In function ‘ndb_cif_init’: cifparse.c:470: warning: cast from pointer to integer of different size cifparse.c: In function ‘ndb_cif_new_datablock’: cifparse.c:538: warning: cast from pointer to integer of different size cifparse.c: In function ‘ndb_cif_get_item_value’: cifparse.c:1478: warning: cast from pointer to integer of different size cifparse.c:1497: warning: cast from pointer to integer of different size rm -f cifparse.a ar rv cifparse.a lex.cif.o cifp.tab.o cifparse.o ar: creating cifparse.a a - lex.cif.o a - cifp.tab.o a - cifparse.o ranlib cifparse.a mv cifparse.a /opt/amber10/lib make[1]: Leaving directory `/opt/amber10/src/cifparse' (cd nab && make install ) make[1]: Entering directory `/opt/amber10/src/nab' gcc -DBINDIR='"."' -DINCDIR='"."' -DLIBDIR='"."' -m64 -DBINTRAJ \ -DCC='"gcc"' -DCPP='"/opt/amber10/bin/ucpp -l"' -DFLIBS='"/opt/amber10/lib/libsym.a /opt/amber10/lib/arpack.a /opt/amber10/lib/lapack.a /opt/amber10/lib/blas.a /opt/amber10/lib/f2c.a "' -o nab nab.c gcc -c -m64 -DBINTRAJ -o nab2c.o nab2c.c flex nablex.l /opt/amber10/bin/yacc -d nabgrm.y /opt/amber10/bin/yacc: w - line 332 of "nabgrm.y", the default action assigns an undefined value to $$ /opt/amber10/bin/yacc: 3 shift/reduce conflicts. gcc -c -m64 -DBINTRAJ -o cgen.o cgen.c (cd ../semantics; make) make[2]: Entering directory `/opt/amber10/src/semantics' gcc -DDATDIR='"/opt/amber10/dat"' -o parse parse.c ./parse *.rules ./parse: 82 symbols. ./parse: 19 types, lastuser = 14, v_error = 14. ./parse: 9 classes. ./parse: 8 kinds. ./parse: 4 accesses. ./parse: 27 attributes. ./parse: 40 rules. ./parse: 40 used symbols. ./parse: 15 used types. ./parse: 7 used classes. ./parse: 7 used kinds. ./parse: 0 errors. make[2]: Leaving directory `/opt/amber10/src/semantics' mv ../semantics/checkexpr.c . gcc -c -m64 -DBINTRAJ -o checkexpr.o checkexpr.c gcc -c -m64 -DBINTRAJ -o dumpnode.o dumpnode.c gcc -c -m64 -DBINTRAJ -o errormsg.o errormsg.c gcc -c -m64 -DBINTRAJ -o fixexpr.o fixexpr.c gcc -c -m64 -DBINTRAJ -o genavscode.o genavscode.c gcc -c -m64 -DBINTRAJ -o node.o node.c gcc -c -m64 -DBINTRAJ -o symbol.o symbol.c gcc -c -m64 -DBINTRAJ -Dflex y.tab.c gcc -o nab2c nab2c.o cgen.o checkexpr.o dumpnode.o errormsg.o fixexpr.o genavscode.o node.o symbol.o y.tab.o ./nab -c allatom_to_dna3.nab gcc -c -m64 -DBINTRAJ -o axis2frame.o axis2frame.c gcc -c -m64 -DBINTRAJ -o binpos.o binpos.c gcc -c -O3 -m64 -DBINTRAJ bonded_atoms.c gcc -c -O3 -m64 -DBINTRAJ -DDATDIR='"/opt/amber10/dat"' boundsutil.c ./nab -c lmod.nab ./nab -c xmin.nab gcc -c -O3 -m64 -DBINTRAJ conjgrad.c gcc -c -m64 -DBINTRAJ -o database.o database.c ./nab -c dna3.nab ./nab -c dna3_to_allatom.nab gcc -c -m64 -DBINTRAJ -o dump.o dump.c flex -t dg_options.l | sed -e 's/yy/dgo/g' -e 's/stdout/nabout/'> lex.dg_options.c gcc -c -O3 -m64 -DBINTRAJ -Dflex embed.c ./nab -c -O0 -DDATDIR='"/opt/amber10/dat"' fd_helix.nab gcc -c -m64 -DBINTRAJ -o frameutil.o frameutil.c gcc -c -DDATDIR='"/opt/amber10/dat"' getdist.c gcc -c -m64 -DBINTRAJ -o hashutil.o hashutil.c gcc -c -m64 -DBINTRAJ -o jacobi.o jacobi.c gcc -c -O3 -m64 -DBINTRAJ lmodC.c gcc -c -m64 -DBINTRAJ -o match.o match.c gcc -c -m64 -DBINTRAJ -o matop.o matop.c gcc -c -m64 -DBINTRAJ -o memutil.o memutil.c gcc -c -O3 -m64 -DBINTRAJ molio.c gcc -c -m64 -DBINTRAJ -o molsurf.o molsurf.c gcc -c -m64 -DBINTRAJ -o molutil.o molutil.c gcc -c -m64 -DBINTRAJ -o dmcsrch.o dmcsrch.c gcc -c -m64 -DBINTRAJ -o nab2avs.o nab2avs.c gcc -c -m64 -DBINTRAJ -o nab2geom.o nab2geom.c gcc -c -O3 -m64 -DBINTRAJ nblist.c gcc -c -O3 -m64 -DBINTRAJ newton.c gcc -c -m64 -DBINTRAJ -o nmode.o nmode.c gcc -c -m64 -DBINTRAJ -o chirvol.o chirvol.c gcc -c -m64 -DBINTRAJ -o pointutil.o pointutil.c gcc -c -m64 -DBINTRAJ -o prm.o prm.c gcc -c -O3 -m64 -DBINTRAJ rand2.c gcc -c -m64 -DBINTRAJ -o regexp.o regexp.c gcc -c -DDATDIR='"/opt/amber10/dat"' reslib.c gcc -c -O3 -m64 -DBINTRAJ sasad.c gcc -c -m64 -DBINTRAJ -o select_atoms.o select_atoms.c flex -t mm_options.l | sed -e 's/yy/mmo/g' -e 's/stdout/nabout/' > lex.mm_options.c gcc -c -O3 -m64 -DBINTRAJ -Dflex sff.c gcc -c -m64 -DBINTRAJ -o stringutil.o stringutil.c gcc -c -m64 -DBINTRAJ -o temputil.o temputil.c gcc -c -m64 -DBINTRAJ -o time.o time.c gcc -c -m64 -DBINTRAJ -o tm_malloc.o tm_malloc.c gcc -c -m64 -DBINTRAJ -o traceback.o traceback.c ./nab -c bdna.nab ./nab -c dg_helix.nab ./nab -c getchivol.nab ./nab -c getres.nab ./nab -c getseq_from_pdb.nab ./nab -c getxyz_from_pdb.nab ./nab -c -DBINDIR='"/opt/amber10/bin"' -DDATDIR='"/opt/amber10/dat"' getpdb_prm.nab ./nab -c getpdb_rlb.nab ./nab -c linkprot.nab ./nab -c link_na.nab ./nab -c -DDATDIR='"/opt/amber10/dat"' na_anal.nab ./nab -c setboundsfromdb.nab ./nab -c setchiplane.nab ./nab -c wc_basepair.nab ./nab -c wc_complement.nab ./nab -c wc_helix.nab gcc -c -O3 -m64 -DBINTRAJ xminC.c ./nab -c yammp.nab rm -f libnab.a ar rv libnab.a allatom_to_dna3.o axis2frame.o binpos.o bonded_atoms.o boundsutil.o lmod.o xmin.o conjgrad.o database.o dna3.o dna3_to_allatom.o dump.o embed.o fd_helix.o frameutil.o getdist.o hashutil.o jacobi.o lmodC.o match.o matop.o memutil.o molio.o molsurf.o molutil.o dmcsrch.o nab2avs.o nab2geom.o nblist.o newton.o nmode.o chirvol.o pointutil.o prm.o rand2.o regexp.o reslib.o sasad.o select_atoms.o sff.o stringutil.o temputil.o time.o tm_malloc.o traceback.o bdna.o dg_helix.o getchivol.o getres.o getseq_from_pdb.o getxyz_from_pdb.o getpdb_prm.o getpdb_rlb.o linkprot.o link_na.o na_anal.o setboundsfromdb.o setchiplane.o wc_basepair.o wc_complement.o wc_helix.o xminC.o yammp.o ar: creating libnab.a a - allatom_to_dna3.o a - axis2frame.o a - binpos.o a - bonded_atoms.o a - boundsutil.o a - lmod.o a - xmin.o a - conjgrad.o a - database.o a - dna3.o a - dna3_to_allatom.o a - dump.o a - embed.o a - fd_helix.o a - frameutil.o a - getdist.o a - hashutil.o a - jacobi.o a - lmodC.o a - match.o a - matop.o a - memutil.o a - molio.o a - molsurf.o a - molutil.o a - dmcsrch.o a - nab2avs.o a - nab2geom.o a - nblist.o a - newton.o a - nmode.o a - chirvol.o a - pointutil.o a - prm.o a - rand2.o a - regexp.o a - reslib.o a - sasad.o a - select_atoms.o a - sff.o a - stringutil.o a - temputil.o a - time.o a - tm_malloc.o a - traceback.o a - bdna.o a - dg_helix.o a - getchivol.o a - getres.o a - getseq_from_pdb.o a - getxyz_from_pdb.o a - getpdb_prm.o a - getpdb_rlb.o a - linkprot.o a - link_na.o a - na_anal.o a - setboundsfromdb.o a - setchiplane.o a - wc_basepair.o a - wc_complement.o a - wc_helix.o a - xminC.o a - yammp.o ranlib libnab.a gcc -DBINDIR='"/opt/amber10/bin"' \ -DINCDIR='"/opt/amber10/include"' \ -DLIBDIR='"/opt/amber10/lib"' \ -m64 -DBINTRAJ -DCC='"gcc"' -DCPP='"/opt/amber10/bin/ucpp -l"' -DFLIBS='"/opt/amber10/lib/libsym.a /opt/amber10/lib/arpack.a /opt/amber10/lib/lapack.a /opt/amber10/lib/blas.a /opt/amber10/lib/f2c.a "' \ -o nab_install nab.c mkdir /opt/amber10/lib /opt/amber10/bin /opt/amber10/include mkdir: cannot create directory `/opt/amber10/lib': File exists mkdir: cannot create directory `/opt/amber10/bin': File exists mkdir: cannot create directory `/opt/amber10/include': File exists make[1]: [install] Error 1 (ignored) mv -f nab_install /opt/amber10/bin/nab mv -f nab2c /opt/amber10/bin mv -f libnab.a /opt/amber10/lib rm -f /opt/amber10/include/nabcode.h /opt/amber10/include/defreal.h /opt/amber10/include/nab.h cp nabcode.h /opt/amber10/include cp nabtypes.h /opt/amber10/include cp defreal.h /opt/amber10/include cp nab.h /opt/amber10/include cp xmin_opt.h lmod_opt.h /opt/amber10/include cp lmodprmtop /opt/amber10/bin make[1]: Leaving directory `/opt/amber10/src/nab' (cd nss && make install ) make[1]: Entering directory `/opt/amber10/src/nss' Makefile:17: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' /opt/amber10/bin/nab -c symop.nab symop.c: In function ‘MAT_ico’: symop.c:219: warning: passing argument 2 of ‘rot4p’ from incompatible pointer type /opt/amber10/bin/nab -c matop.c /opt/amber10/bin/nab -c tss.c ar rv libsym.a symop.o matop.o tss.o ar: creating libsym.a a - symop.o a - matop.o a - tss.o ranlib libsym.a cp -p libsym.a /opt/amber10/lib /opt/amber10/bin/nab -c matextract.nab /opt/amber10/bin/nab -o matextract matextract.o libsym.a /opt/amber10/bin/nab -c matgen.nab /opt/amber10/bin/nab -o matgen matgen.o libsym.a /opt/amber10/bin/nab -c matmerge.nab /opt/amber10/bin/nab -o matmerge matmerge.o libsym.a /opt/amber10/bin/nab -c matmul.nab /opt/amber10/bin/nab -o matmul matmul.o libsym.a /opt/amber10/bin/nab -c transform.nab transform.c: In function ‘main’: transform.c:76: warning: passing argument 3 of ‘setxyz_from_mol’ from incompatible pointer type transform.c:79: warning: passing argument 3 of ‘setmol_from_xyz’ from incompatible pointer type transform.c:115: warning: passing argument 2 of ‘transformpts’ from incompatible pointer type /opt/amber10/bin/nab -o transform transform.o libsym.a /opt/amber10/bin/nab -c tss_init.nab /opt/amber10/bin/nab -o tss_init tss_init.o libsym.a /opt/amber10/bin/nab -c tss_main.nab tss_main.c: In function ‘main’: tss_main.c:300: warning: passing argument 3 of ‘setxyz_from_mol’ from incompatible pointer type tss_main.c:301: warning: passing argument 2 of ‘transformpts’ from incompatible pointer type tss_main.c:302: warning: passing argument 3 of ‘setmol_from_xyz’ from incompatible pointer type /opt/amber10/bin/nab -o tss_main tss_main.o libsym.a tss_main.o: In function `main': tss_main.c:(.text+0x9f9): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /opt/amber10/bin/nab -c tss_next.nab /opt/amber10/bin/nab -o tss_next tss_next.o libsym.a cp -p matextract matgen matmerge matmul \ transform tss_init tss_main \ tss_next /opt/amber10/bin cp -p libsym.a /opt/amber10/lib make[1]: Leaving directory `/opt/amber10/src/nss' (cd antechamber && make install ) make[1]: Entering directory `/opt/amber10/src/antechamber' Makefile:219: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' am1bcc.c gcc am1bcc.o -lm -o am1bcc gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' acdoctor.c gcc acdoctor.o -lm -o acdoctor gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' antechamber.c gcc antechamber.o -lm -o antechamber gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' atomtype.c gcc atomtype.o -lm -o atomtype gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' bondtype.c gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' ncsu-penalties.c gcc ncsu-penalties.o bondtype.o -o bondtype gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' charmmgen.c gcc charmmgen.o -lm -o charmmgen gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' database.c gcc database.o -lm -o database gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' espgen.c gcc espgen.o -o espgen gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' parmcal.c gcc parmcal.o -lm -o parmcal gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' parmchk.c gcc parmchk.o -lm -o parmchk gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' prepgen.c gcc prepgen.o -lm -o prepgen gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' residuegen.c gcc residuegen.o -lm -o residuegen gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' respgen.c gcc respgen.o -lm -o respgen gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' translate.c gcc translate.o -lm -o translate gcc -m64 -DBINTRAJ -c -DDATDIR='"/opt/amber10/dat"' -DBINDIR='"/opt/amber10/bin"' top2mol2.c gcc top2mol2.o -lm -o top2mol2 sed -e "s?BINDIR?/opt/amber10/bin?" mopac.sh > /opt/amber10/bin/mopac.sh chmod +x /opt/amber10/bin/mopac.sh mv -f am1bcc acdoctor antechamber atomtype bondtype charmmgen database espgen parmcal parmchk prepgen residuegen respgen translate top2mol2 /opt/amber10/bin make[1]: Leaving directory `/opt/amber10/src/antechamber' (cd mopac6/src && make hasG77 ) make[1]: Entering directory `/opt/amber10/src/mopac6/src' g77 -c -O2 -fno-automatic -finit-local-zero -o aababc.o aababc.f g77 -c -O2 -fno-automatic -finit-local-zero -o readmo.o readmo.f g77 -c -O2 -fno-automatic -finit-local-zero -o writmo.o writmo.f g77 -c -O2 -fno-automatic -finit-local-zero -o mopac.o mopac.f g77 -c -O2 -fno-automatic -finit-local-zero -o analyt.o analyt.f g77 -c -O2 -fno-automatic -finit-local-zero -o anavib.o anavib.f g77 -c -O2 -fno-automatic -finit-local-zero -o axis.o axis.f g77 -c -O2 -fno-automatic -finit-local-zero -o block.o block.f g77 -c -O2 -fno-automatic -finit-local-zero -o bonds.o bonds.f g77 -c -O2 -fno-automatic -finit-local-zero -o brlzon.o brlzon.f g77 -c -O2 -fno-automatic -finit-local-zero -o calpar.o calpar.f g77 -c -O2 -fno-automatic -finit-local-zero -o capcor.o capcor.f g77 -c -O2 -fno-automatic -finit-local-zero -o cdiag.o cdiag.f g77 -c -O2 -fno-automatic -finit-local-zero -o chrge.o chrge.f g77 -c -O2 -fno-automatic -finit-local-zero -o cnvg.o cnvg.f g77 -c -O2 -fno-automatic -finit-local-zero -o compfg.o compfg.f g77 -c -O2 -fno-automatic -finit-local-zero -o datin.o datin.f g77 -c -O2 -fno-automatic -finit-local-zero -o dcart.o dcart.f g77 -c -O2 -fno-automatic -finit-local-zero -o delmol.o delmol.f g77 -c -O2 -fno-automatic -finit-local-zero -o delri.o delri.f g77 -c -O2 -fno-automatic -finit-local-zero -o denrot.o denrot.f g77 -c -O2 -fno-automatic -finit-local-zero -o densit.o densit.f g77 -c -O2 -fno-automatic -finit-local-zero -o depvar.o depvar.f g77 -c -O2 -fno-automatic -finit-local-zero -o deri0.o deri0.f g77 -c -O2 -fno-automatic -finit-local-zero -o deri1.o deri1.f g77 -c -O2 -fno-automatic -finit-local-zero -o deri2.o deri2.f g77 -c -O2 -fno-automatic -finit-local-zero -o deri21.o deri21.f g77 -c -O2 -fno-automatic -finit-local-zero -o deri22.o deri22.f g77 -c -O2 -fno-automatic -finit-local-zero -o deri23.o deri23.f g77 -c -O2 -fno-automatic -finit-local-zero -o deritr.o deritr.f g77 -c -O2 -fno-automatic -finit-local-zero -o deriv.o deriv.f g77 -c -O2 -fno-automatic -finit-local-zero -o dernvo.o dernvo.f g77 -c -O2 -fno-automatic -finit-local-zero -o ders.o ders.f g77 -c -O2 -fno-automatic -finit-local-zero -o dfock2.o dfock2.f g77 -c -O2 -fno-automatic -finit-local-zero -o dfpsav.o dfpsav.f g77 -c -O2 -fno-automatic -finit-local-zero -o diag.o diag.f g77 -c -O2 -fno-automatic -finit-local-zero -o diat.o diat.f g77 -c -O2 -fno-automatic -finit-local-zero -o diat2.o diat2.f g77 -c -O2 -fno-automatic -finit-local-zero -o diis.o diis.f g77 -c -O2 -fno-automatic -finit-local-zero -o dijkl1.o dijkl1.f g77 -c -O2 -fno-automatic -finit-local-zero -o dijkl2.o dijkl2.f g77 -c -O2 -fno-automatic -finit-local-zero -o dipind.o dipind.f g77 -c -O2 -fno-automatic -finit-local-zero -o dipole.o dipole.f g77 -c -O2 -fno-automatic -finit-local-zero -o dofs.o dofs.f g77 -c -O2 -fno-automatic -finit-local-zero -o dot.o dot.f g77 -c -O2 -fno-automatic -finit-local-zero -o drc.o drc.f g77 -c -O2 -fno-automatic -finit-local-zero -o drcout.o drcout.f g77 -c -O2 -fno-automatic -finit-local-zero -o ef.o ef.f g77 -c -O2 -fno-automatic -finit-local-zero -o enpart.o enpart.f g77 -c -O2 -fno-automatic -finit-local-zero -o exchng.o exchng.f g77 -c -O2 -fno-automatic -finit-local-zero -o ffhpol.o ffhpol.f g77 -c -O2 -fno-automatic -finit-local-zero -o flepo.o flepo.f g77 -c -O2 -fno-automatic -finit-local-zero -o fmat.o fmat.f g77 -c -O2 -fno-automatic -finit-local-zero -o fock1.o fock1.f g77 -c -O2 -fno-automatic -finit-local-zero -o fock2.o fock2.f g77 -c -O2 -fno-automatic -finit-local-zero -o force.o force.f g77 -c -O2 -fno-automatic -finit-local-zero -o formxy.o formxy.f g77 -c -O2 -fno-automatic -finit-local-zero -o forsav.o forsav.f g77 -c -O2 -fno-automatic -finit-local-zero -o frame.o frame.f g77 -c -O2 -fno-automatic -finit-local-zero -o freqcy.o freqcy.f g77 -c -O2 -fno-automatic -finit-local-zero -o geout.o geout.f g77 -c -O2 -fno-automatic -finit-local-zero -o geoutg.o geoutg.f g77 -c -O2 -fno-automatic -finit-local-zero -o getgeg.o getgeg.f g77 -c -O2 -fno-automatic -finit-local-zero -o getgeo.o getgeo.f g77 -c -O2 -fno-automatic -finit-local-zero -o getsym.o getsym.f g77 -c -O2 -fno-automatic -finit-local-zero -o gettxt.o gettxt.f g77 -c -O2 -fno-automatic -finit-local-zero -o gmetry.o gmetry.f g77 -c -O2 -fno-automatic -finit-local-zero -o gover.o gover.f g77 -c -O2 -fno-automatic -finit-local-zero -o grid.o grid.f g77 -c -O2 -fno-automatic -finit-local-zero -o h1elec.o h1elec.f g77 -c -O2 -fno-automatic -finit-local-zero -o haddon.o haddon.f g77 -c -O2 -fno-automatic -finit-local-zero -o hcore.o hcore.f g77 -c -O2 -fno-automatic -finit-local-zero -o helect.o helect.f g77 -c -O2 -fno-automatic -finit-local-zero -o hqrii.o hqrii.f g77 -c -O2 -fno-automatic -finit-local-zero -o ijkl.o ijkl.f g77 -c -O2 -fno-automatic -finit-local-zero -o interp.o interp.f g77 -c -O2 -fno-automatic -finit-local-zero -o iter.o iter.f g77 -c -O2 -fno-automatic -finit-local-zero -o jcarin.o jcarin.f g77 -c -O2 -fno-automatic -finit-local-zero -o linmin.o linmin.f g77 -c -O2 -fno-automatic -finit-local-zero -o local.o local.f g77 -c -O2 -fno-automatic -finit-local-zero -o locmin.o locmin.f g77 -c -O2 -fno-automatic -finit-local-zero -o mamult.o mamult.f g77 -c -O2 -fno-automatic -finit-local-zero -o matout.o matout.f g77 -c -O2 -fno-automatic -finit-local-zero -o matpak.o matpak.f g77 -c -O2 -fno-automatic -finit-local-zero -o meci.o meci.f g77 -c -O2 -fno-automatic -finit-local-zero -o mecid.o mecid.f g77 -c -O2 -fno-automatic -finit-local-zero -o mecih.o mecih.f g77 -c -O2 -fno-automatic -finit-local-zero -o mecip.o mecip.f g77 -c -O2 -fno-automatic -finit-local-zero -o moldat.o moldat.f g77 -c -O2 -fno-automatic -finit-local-zero -o molval.o molval.f g77 -c -O2 -fno-automatic -finit-local-zero -o mullik.o mullik.f g77 -c -O2 -fno-automatic -finit-local-zero -o mult.o mult.f g77 -c -O2 -fno-automatic -finit-local-zero -o nllsq.o nllsq.f g77 -c -O2 -fno-automatic -finit-local-zero -o nuchar.o nuchar.f g77 -c -O2 -fno-automatic -finit-local-zero -o parsav.o parsav.f g77 -c -O2 -fno-automatic -finit-local-zero -o partxy.o partxy.f g77 -c -O2 -fno-automatic -finit-local-zero -o pathk.o pathk.f g77 -c -O2 -fno-automatic -finit-local-zero -o paths.o paths.f g77 -c -O2 -fno-automatic -finit-local-zero -o perm.o perm.f g77 -c -O2 -fno-automatic -finit-local-zero -o polar.o polar.f g77 -c -O2 -fno-automatic -finit-local-zero -o powsav.o powsav.f g77 -c -O2 -fno-automatic -finit-local-zero -o powsq.o powsq.f g77 -c -O2 -fno-automatic -finit-local-zero -o prtdrc.o prtdrc.f g77 -c -O2 -fno-automatic -finit-local-zero -o quadr.o quadr.f g77 -c -O2 -fno-automatic -finit-local-zero -o react1.o react1.f g77 -c -O2 -fno-automatic -finit-local-zero -o reada.o reada.f g77 -c -O2 -fno-automatic -finit-local-zero -o refer.o refer.f g77 -c -O2 -fno-automatic -finit-local-zero -o repp.o repp.f g77 -c -O2 -fno-automatic -finit-local-zero -o rotat.o rotat.f g77 -c -O2 -fno-automatic -finit-local-zero -o rotate.o rotate.f g77 -c -O2 -fno-automatic -finit-local-zero -o rsp.o rsp.f g77 -c -O2 -fno-automatic -finit-local-zero -o search.o search.f g77 -c -O2 -fno-automatic -finit-local-zero -o second.o second.f g77 -c -O2 -fno-automatic -finit-local-zero -o setupg.o setupg.f g77 -c -O2 -fno-automatic -finit-local-zero -o solrot.o solrot.f g77 -c -O2 -fno-automatic -finit-local-zero -o swap.o swap.f g77 -c -O2 -fno-automatic -finit-local-zero -o symtry.o symtry.f g77 -c -O2 -fno-automatic -finit-local-zero -o thermo.o thermo.f g77 -c -O2 -fno-automatic -finit-local-zero -o timer.o timer.f g77 -c -O2 -fno-automatic -finit-local-zero -o update.o update.f g77 -c -O2 -fno-automatic -finit-local-zero -o vecprt.o vecprt.f g77 -c -O2 -fno-automatic -finit-local-zero -o wrtkey.o wrtkey.f g77 -c -O2 -fno-automatic -finit-local-zero -o wrttxt.o wrttxt.f g77 -c -O2 -fno-automatic -finit-local-zero -o xyzint.o xyzint.f g77 aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o -o mopac mv mopac /opt/amber10/bin make[1]: Leaving directory `/opt/amber10/src/mopac6/src' (cd resp && make hasG77 ) make[1]: Entering directory `/opt/amber10/src/resp' g77 -c -O2 -fno-automatic -finit-local-zero -o lapack.o lapack.f g77 -c -O2 -fno-automatic -finit-local-zero -o resp.o resp.f g77 lapack.o resp.o -o resp mv resp /opt/amber10/bin make[1]: Leaving directory `/opt/amber10/src/resp' (cd ptraj && make install ) make[1]: Entering directory `/opt/amber10/src/ptraj' Makefile:24: warning: overriding commands for target `.c.o' ../config.h:99: warning: ignoring old commands for target `.c.o' cd pdb; make make[2]: Entering directory `/opt/amber10/src/ptraj/pdb' gcc -c -m64 -DBINTRAJ -o pdbrun.o pdbrun.c gcc -c -m64 -DBINTRAJ -o pdb_read.o pdb_read.c gcc -c -m64 -DBINTRAJ -o pdb_sprntf.o pdb_sprntf.c gcc -c -m64 -DBINTRAJ -o pdb_sscanf.o pdb_sscanf.c gcc -c -m64 -DBINTRAJ -o pdb_write.o pdb_write.c gcc -c -m64 -DBINTRAJ -o ms.o ms.c ar rv libpdb.a pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o ms.o ar: creating libpdb.a a - pdbrun.o a - pdb_read.o a - pdb_sprntf.o a - pdb_sscanf.o a - pdb_write.o a - ms.o ranlib libpdb.a mv libpdb.a /opt/amber10/lib make[2]: Leaving directory `/opt/amber10/src/ptraj/pdb' cd ../netcdf/src; make install make[2]: Entering directory `/opt/amber10/src/netcdf/src' Making install in libsrc make[3]: Entering directory `/opt/amber10/src/netcdf/src/libsrc' depbase=`echo attr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT attr.lo -MD -MP -MF "$depbase.Tpo" -c -o attr.lo attr.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT attr.lo -MD -MP -MF .deps/attr.Tpo -c attr.c -o attr.o depbase=`echo ncx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT ncx.lo -MD -MP -MF "$depbase.Tpo" -c -o ncx.lo ncx.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT ncx.lo -MD -MP -MF .deps/ncx.Tpo -c ncx.c -o ncx.o depbase=`echo putget.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT putget.lo -MD -MP -MF "$depbase.Tpo" -c -o putget.lo putget.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT putget.lo -MD -MP -MF .deps/putget.Tpo -c putget.c -o putget.o depbase=`echo dim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT dim.lo -MD -MP -MF "$depbase.Tpo" -c -o dim.lo dim.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT dim.lo -MD -MP -MF .deps/dim.Tpo -c dim.c -o dim.o depbase=`echo error.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT error.lo -MD -MP -MF "$depbase.Tpo" -c -o error.lo error.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT error.lo -MD -MP -MF .deps/error.Tpo -c error.c -o error.o depbase=`echo libvers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT libvers.lo -MD -MP -MF "$depbase.Tpo" -c -o libvers.lo libvers.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT libvers.lo -MD -MP -MF .deps/libvers.Tpo -c libvers.c -o libvers.o depbase=`echo nc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT nc.lo -MD -MP -MF "$depbase.Tpo" -c -o nc.lo nc.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT nc.lo -MD -MP -MF .deps/nc.Tpo -c nc.c -o nc.o depbase=`echo string.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT string.lo -MD -MP -MF "$depbase.Tpo" -c -o string.lo string.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT string.lo -MD -MP -MF .deps/string.Tpo -c string.c -o string.o depbase=`echo v1hpg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT v1hpg.lo -MD -MP -MF "$depbase.Tpo" -c -o v1hpg.lo v1hpg.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT v1hpg.lo -MD -MP -MF .deps/v1hpg.Tpo -c v1hpg.c -o v1hpg.o depbase=`echo var.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT var.lo -MD -MP -MF "$depbase.Tpo" -c -o var.lo var.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT var.lo -MD -MP -MF .deps/var.Tpo -c var.c -o var.o depbase=`echo posixio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT posixio.lo -MD -MP -MF "$depbase.Tpo" -c -o posixio.lo posixio.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT posixio.lo -MD -MP -MF .deps/posixio.Tpo -c posixio.c -o posixio.o depbase=`echo v2i.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \ if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT v2i.lo -MD -MP -MF "$depbase.Tpo" -c -o v2i.lo v2i.c; \ then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT v2i.lo -MD -MP -MF .deps/v2i.Tpo -c v2i.c -o v2i.o /bin/bash ../libtool --tag=CC --mode=link gcc -m64 -DBINTRAJ -o libnetcdf2.la v2i.lo mkdir .libs ar cru .libs/libnetcdf2.a v2i.o ranlib .libs/libnetcdf2.a creating libnetcdf2.la (cd .libs && rm -f libnetcdf2.la && ln -s ../libnetcdf2.la libnetcdf2.la) /bin/bash ../libtool --tag=CC --mode=link gcc -m64 -DBINTRAJ -o libnetcdf.la -rpath /opt/amber10/src/netcdf/lib -version-info 4:0:0 -no-undefined attr.lo ncx.lo putget.lo dim.lo error.lo libvers.lo nc.lo string.lo v1hpg.lo var.lo posixio.lo libnetcdf2.la rm -fr .libs/libnetcdf.lax mkdir .libs/libnetcdf.lax rm -fr .libs/libnetcdf.lax/libnetcdf2.a mkdir .libs/libnetcdf.lax/libnetcdf2.a (cd .libs/libnetcdf.lax/libnetcdf2.a && ar x /opt/amber10/src/netcdf/src/libsrc/./.libs/libnetcdf2.a) ar cru .libs/libnetcdf.a attr.o ncx.o putget.o dim.o error.o libvers.o nc.o string.o v1hpg.o var.o posixio.o .libs/libnetcdf.lax/libnetcdf2.a/v2i.o ranlib .libs/libnetcdf.a rm -fr .libs/libnetcdf.lax creating libnetcdf.la (cd .libs && rm -f libnetcdf.la && ln -s ../libnetcdf.la libnetcdf.la) make[4]: Entering directory `/opt/amber10/src/netcdf/src/libsrc' test -z "/opt/amber10/src/netcdf/lib" || mkdir -p -- "/opt/amber10/src/netcdf/lib" /bin/bash ../libtool --mode=install /usr/bin/install -c 'libnetcdf.la' '/opt/amber10/src/netcdf/lib/libnetcdf.la' /usr/bin/install -c .libs/libnetcdf.lai /opt/amber10/src/netcdf/lib/libnetcdf.la /usr/bin/install -c .libs/libnetcdf.a /opt/amber10/src/netcdf/lib/libnetcdf.a chmod 644 /opt/amber10/src/netcdf/lib/libnetcdf.a ranlib /opt/amber10/src/netcdf/lib/libnetcdf.a PATH="$PATH:/sbin" ldconfig -n /opt/amber10/src/netcdf/lib ---------------------------------------------------------------------- Libraries have been installed in: /opt/amber10/src/netcdf/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,--rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- test -z "/opt/amber10/src/netcdf/include" || mkdir -p -- "/opt/amber10/src/netcdf/include" /usr/bin/install -c -m 644 'netcdf.h' '/opt/amber10/src/netcdf/include/netcdf.h' test -z "/opt/amber10/src/netcdf/share/man/man3" || mkdir -p -- "/opt/amber10/src/netcdf/share/man/man3" /usr/bin/install -c -m 644 './netcdf.3' '/opt/amber10/src/netcdf/share/man/man3/netcdf.3' make[4]: Leaving directory `/opt/amber10/src/netcdf/src/libsrc' make[3]: Leaving directory `/opt/amber10/src/netcdf/src/libsrc' Making install in nctest make[3]: Entering directory `/opt/amber10/src/netcdf/src/nctest' make[4]: Entering directory `/opt/amber10/src/netcdf/src/nctest' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/opt/amber10/src/netcdf/src/nctest' make[3]: Leaving directory `/opt/amber10/src/netcdf/src/nctest' Making install in ncgen make[3]: Entering directory `/opt/amber10/src/netcdf/src/ncgen' depbase=`echo main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT main.o -MD -MP -MF "$depbase.Tpo" -c -o main.o main.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo load.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT load.o -MD -MP -MF "$depbase.Tpo" -c -o load.o load.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo ncgentab.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT ncgentab.o -MD -MP -MF "$depbase.Tpo" -c -o ncgentab.o ncgentab.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo escapes.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT escapes.o -MD -MP -MF "$depbase.Tpo" -c -o escapes.o escapes.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo getfill.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT getfill.o -MD -MP -MF "$depbase.Tpo" -c -o getfill.o getfill.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo init.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT init.o -MD -MP -MF "$depbase.Tpo" -c -o init.o init.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo genlib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT genlib.o -MD -MP -MF "$depbase.Tpo" -c -o genlib.o genlib.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi /bin/bash ../libtool --tag=CC --mode=link gcc -m64 -DBINTRAJ -o ncgen main.o load.o ncgentab.o escapes.o getfill.o init.o genlib.o ../libsrc/libnetcdf.la mkdir .libs gcc -m64 -DBINTRAJ -o ncgen main.o load.o ncgentab.o escapes.o getfill.o init.o genlib.o ../libsrc/.libs/libnetcdf.a make[4]: Entering directory `/opt/amber10/src/netcdf/src/ncgen' test -z "/opt/amber10/src/netcdf/bin" || mkdir -p -- "/opt/amber10/src/netcdf/bin" /bin/bash ../libtool --mode=install /usr/bin/install -c 'ncgen' '/opt/amber10/src/netcdf/bin/ncgen' /usr/bin/install -c ncgen /opt/amber10/src/netcdf/bin/ncgen test -z "/opt/amber10/src/netcdf/share/man/man1" || mkdir -p -- "/opt/amber10/src/netcdf/share/man/man1" /usr/bin/install -c -m 644 './ncgen.1' '/opt/amber10/src/netcdf/share/man/man1/ncgen.1' make[4]: Leaving directory `/opt/amber10/src/netcdf/src/ncgen' make[3]: Leaving directory `/opt/amber10/src/netcdf/src/ncgen' Making install in ncdump make[3]: Entering directory `/opt/amber10/src/netcdf/src/ncdump' depbase=`echo ncdump.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT ncdump.o -MD -MP -MF "$depbase.Tpo" -c -o ncdump.o ncdump.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo vardata.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT vardata.o -MD -MP -MF "$depbase.Tpo" -c -o vardata.o vardata.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo dumplib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -I../libsrc -m64 -DBINTRAJ -MT dumplib.o -MD -MP -MF "$depbase.Tpo" -c -o dumplib.o dumplib.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi /bin/bash ../libtool --tag=CC --mode=link gcc -m64 -DBINTRAJ -o ncdump ncdump.o vardata.o dumplib.o -lm ../libsrc/libnetcdf.la mkdir .libs gcc -m64 -DBINTRAJ -o ncdump ncdump.o vardata.o dumplib.o -lm ../libsrc/.libs/libnetcdf.a make[4]: Entering directory `/opt/amber10/src/netcdf/src/ncdump' test -z "/opt/amber10/src/netcdf/bin" || mkdir -p -- "/opt/amber10/src/netcdf/bin" /bin/bash ../libtool --mode=install /usr/bin/install -c 'ncdump' '/opt/amber10/src/netcdf/bin/ncdump' /usr/bin/install -c ncdump /opt/amber10/src/netcdf/bin/ncdump test -z "/opt/amber10/src/netcdf/share/man/man1" || mkdir -p -- "/opt/amber10/src/netcdf/share/man/man1" /usr/bin/install -c -m 644 './ncdump.1' '/opt/amber10/src/netcdf/share/man/man1/ncdump.1' make[4]: Leaving directory `/opt/amber10/src/netcdf/src/ncdump' make[3]: Leaving directory `/opt/amber10/src/netcdf/src/ncdump' Making install in nc_test make[3]: Entering directory `/opt/amber10/src/netcdf/src/nc_test' make[4]: Entering directory `/opt/amber10/src/netcdf/src/nc_test' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/opt/amber10/src/netcdf/src/nc_test' make[3]: Leaving directory `/opt/amber10/src/netcdf/src/nc_test' Making install in examples make[3]: Entering directory `/opt/amber10/src/netcdf/src/examples' Making install in C make[4]: Entering directory `/opt/amber10/src/netcdf/src/examples/C' make[5]: Entering directory `/opt/amber10/src/netcdf/src/examples/C' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/opt/amber10/src/netcdf/src/examples/C' make[4]: Leaving directory `/opt/amber10/src/netcdf/src/examples/C' Making install in CDL make[4]: Entering directory `/opt/amber10/src/netcdf/src/examples/CDL' make[5]: Entering directory `/opt/amber10/src/netcdf/src/examples/CDL' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/opt/amber10/src/netcdf/src/examples/CDL' make[4]: Leaving directory `/opt/amber10/src/netcdf/src/examples/CDL' make[4]: Entering directory `/opt/amber10/src/netcdf/src/examples' make[5]: Entering directory `/opt/amber10/src/netcdf/src/examples' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/opt/amber10/src/netcdf/src/examples' make[4]: Leaving directory `/opt/amber10/src/netcdf/src/examples' make[3]: Leaving directory `/opt/amber10/src/netcdf/src/examples' make[3]: Entering directory `/opt/amber10/src/netcdf/src' make[4]: Entering directory `/opt/amber10/src/netcdf/src' make[4]: Nothing to be done for `install-exec-am'. make install-data-hook make[5]: Entering directory `/opt/amber10/src/netcdf/src' +-------------------------------------------------------------+ | CAUTION: | | | | If you have not already run "make check", then we strongly | | recommend you do so. It does not take very long. | | | | Before using netCDF to store important data, test your | | build with "make check". | | | | NetCDF is tested nightly on many platforms at Unidata | | but your platform is probably different in some ways. | | | | If any tests fail, please see the netCDF web site: | | http://www.unidata.ucar.edu/software/netcdf/ | | | | NetCDF is developed and maintained at the Unidata Program | | Center. Unidata provides a broad array of data and software | | tools for use in geoscience education and research. | | http://www.unidata.ucar.edu | +-------------------------------------------------------------+ make[5]: Leaving directory `/opt/amber10/src/netcdf/src' make[4]: Leaving directory `/opt/amber10/src/netcdf/src' make[3]: Leaving directory `/opt/amber10/src/netcdf/src' make[2]: Leaving directory `/opt/amber10/src/netcdf/src' gcc -c -m64 -DBINTRAJ -o main.o main.c gcc -c -m64 -DBINTRAJ -o rdparm.o rdparm.c gcc -c -m64 -DBINTRAJ -o dispatch.o dispatch.c gcc -c -m64 -DBINTRAJ -o help.o help.c gcc -c -m64 -DBINTRAJ -o utility.o utility.c gcc -c -m64 -DBINTRAJ -o second.o second.c gcc -c -m64 -DBINTRAJ -o io.o io.c gcc -c -m64 -DBINTRAJ -o trajectory.o trajectory.c gcc -c -m64 -DBINTRAJ -o evec.o evec.c gcc -c -m64 -DBINTRAJ -o torsion.o torsion.c gcc -c -m64 -DBINTRAJ -o mask.o mask.c gcc -c -m64 -DBINTRAJ -o rms.o rms.c gcc -c -m64 -DBINTRAJ -o display.o display.c gcc -c -m64 -DBINTRAJ -o interface.o interface.c gcc -c -m64 -DBINTRAJ -o energy.o energy.c gcc -c -m64 -DBINTRAJ -o experimental.o experimental.c gcc -c -m64 -DBINTRAJ -o ptraj.o ptraj.c gcc -c -m64 -DBINTRAJ -o actions.o actions.c gcc -c -m64 -DBINTRAJ -o analyze.o analyze.c gcc -c -m64 -DBINTRAJ -o thermo.o thermo.c gcc -c -m64 -DBINTRAJ -o pubfft.o pubfft.c gcc -c -m64 -DBINTRAJ -o cluster.o cluster.c gcc -c -m64 -DBINTRAJ -o clusterLib.o clusterLib.c gcc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o /opt/amber10/lib/libpdb.a /opt/amber10/lib/libsym.a /opt/amber10/lib/arpack.a /opt/amber10/lib/lapack.a /opt/amber10/lib/blas.a /opt/amber10/lib/f2c.a ../netcdf/lib/libnetcdf.a -lm gcc -o ptraj main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o /opt/amber10/lib/libpdb.a /opt/amber10/lib/libsym.a /opt/amber10/lib/arpack.a /opt/amber10/lib/lapack.a /opt/amber10/lib/blas.a /opt/amber10/lib/f2c.a ../netcdf/lib/libnetcdf.a -lm /bin/mv rdparm ptraj /opt/amber10/bin make[1]: Leaving directory `/opt/amber10/src/ptraj' (cd reduce && make install ) make[1]: Entering directory `/opt/amber10/src/reduce' installing /toolclasses... make[2]: Entering directory `/opt/amber10/src/reduce/toolclasses' g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c UseCount.cpp -o UseCount.o g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Point3d.cpp -o Point3d.o g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Stringclass.cpp -o Stringclass.o g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Hash.cpp -o Hash.o g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c utility.cpp -o utility.o g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c column_sprintf.cpp -o column_sprintf.o g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c column_sscanf.cpp -o column_sscanf.o g++ -O -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c DisjointSets.cpp -o DisjointSets.o Loading libtoolclasses.a ... done make[2]: Leaving directory `/opt/amber10/src/reduce/toolclasses' installing /libpdb... make[2]: Entering directory `/opt/amber10/src/reduce/libpdb' g++ -O -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_read.cpp -o pdb_read.o g++ -O -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_sprntf.cpp -o pdb_sprntf.o g++ -O -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_sscanf.cpp -o pdb_sscanf.o g++ -O -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_chars.cpp -o pdb_chars.o g++ -O -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_type.cpp -o pdb_type.o g++ -O -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb++.cpp -o pdb++.o g++ -O -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdbinput.cpp -o pdbinput.o Loading libpdb++.a ... done make[2]: Leaving directory `/opt/amber10/src/reduce/libpdb' installing /reduce_src... make[2]: Entering directory `/opt/amber10/src/reduce/reduce_src' g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o GraphToHoldScores.o GraphToHoldScores.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o reduce.o reduce.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o CTab.o CTab.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o ElementInfo.o ElementInfo.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o StdResH.o StdResH.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o ResBlk.o ResBlk.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o AtomConn.o AtomConn.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o AtomPositions.o AtomPositions.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o DotSph.o DotSph.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o Mover.o Mover.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o RotMethyl.o RotMethyl.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o RotDonor.o RotDonor.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o FlipMemo.o FlipMemo.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o CliqueList.o CliqueList.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o AtomDescr.o AtomDescr.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o PDBrec.o PDBrec.cpp g++ -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o MoveableNode.o MoveableNode.cpp gcc -c -O3 -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/opt/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses -o hybrid_36_c.o hybrid_36_c.c g++ -o reduce GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o Mover.o RotMethyl.o RotDonor.o FlipMemo.o CliqueList.o AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o -L../libpdb -lpdb++ -L../toolclasses -ltoolclasses -lm mv reduce /opt/amber10/bin gunzip -c -d ../reduce_wwPDB_het_dict.txt.gz > /opt/amber10/dat/reduce_wwPDB_het_dict.txt make[2]: Leaving directory `/opt/amber10/src/reduce/reduce_src' make[1]: Leaving directory `/opt/amber10/src/reduce' (cd leap && make install ) make[1]: Entering directory `/opt/amber10/src/leap' Compiling basic programs cd src/leap; make installteLeap make[2]: Entering directory `/opt/amber10/src/leap/src/leap' gcc -c -m64 -DBINTRAJ -o basics.o basics.c gcc -c -m64 -DBINTRAJ -o sysdepend.o sysdepend.c gcc -c -m64 -DBINTRAJ -o stringExtra.o stringExtra.c gcc -c -m64 -DBINTRAJ -o varArray.o varArray.c gcc -c -m64 -DBINTRAJ -o getline.o getline.c gcc -c -m64 -DBINTRAJ -o avl.o avl.c gcc -c -m64 -DBINTRAJ -o pdb_format.o pdb_format.c gcc -c -m64 -DBINTRAJ -o pdb_read.o pdb_read.c gcc -c -m64 -DBINTRAJ -o pdb_sprntf.o pdb_sprntf.c gcc -c -m64 -DBINTRAJ -o pdb_sscanf.o pdb_sscanf.c gcc -c -m64 -DBINTRAJ -o pdb_write.o pdb_write.c gcc -c -m64 -DBINTRAJ -o vector.o vector.c gcc -c -m64 -DBINTRAJ -o zMatrix.o zMatrix.c gcc -c -m64 -DBINTRAJ -o sort.o sort.c gcc -c -m64 -DBINTRAJ -o bag.o bag.c gcc -c -m64 -DBINTRAJ -o hash.o hash.c gcc -c -m64 -DBINTRAJ -o dictionary.o dictionary.c gcc -c -m64 -DBINTRAJ -o database.o database.c gcc -c -m64 -DBINTRAJ -o nVector.o nVector.c gcc -c -m64 -DBINTRAJ -o ring.o ring.c gcc -c -m64 -DBINTRAJ -o matrix.o matrix.c gcc -c -m64 -DBINTRAJ -o fortran.o fortran.c gcc -c -m64 -DBINTRAJ -o displayer.o displayer.c gcc -c -m64 -DBINTRAJ -o assoc.o assoc.c gcc -c -m64 -DBINTRAJ -o atom.o atom.c gcc -c -m64 -DBINTRAJ -o byteArray.o byteArray.c gcc -c -m64 -DBINTRAJ -o collection.o collection.c gcc -c -m64 -DBINTRAJ -o container.o container.c gcc -c -m64 -DBINTRAJ -o internal.o internal.c gcc -c -m64 -DBINTRAJ -o list.o list.c gcc -c -m64 -DBINTRAJ -o loop.o loop.c gcc -c -m64 -DBINTRAJ -o molecule.o molecule.c gcc -c -m64 -DBINTRAJ -o oDouble.o oDouble.c gcc -c -m64 -DBINTRAJ -o oInteger.o oInteger.c gcc -c -m64 -DBINTRAJ -o oString.o oString.c gcc -c -m64 -DBINTRAJ -o objekt.o objekt.c gcc -c -m64 -DBINTRAJ -o parmSet.o parmSet.c gcc -c -m64 -DBINTRAJ -o residue.o residue.c residue.c: In function ‘ResidueConnect’: residue.c:336: warning: passing argument 1 of ‘AtomBondTo’ from incompatible pointer type residue.c:336: warning: passing argument 2 of ‘AtomBondTo’ from incompatible pointer type residue.c: In function ‘ResidueMutate’: residue.c:464: warning: passing argument 1 of ‘BuildFixInternals’ from incompatible pointer type gcc -c -m64 -DBINTRAJ -o unit.o unit.c gcc -c -m64 -DBINTRAJ -o unitio.o unitio.c unitio.c: In function ‘zUnitIOSaveAmberParmFormat’: unitio.c:4056: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type unitio.c:4056: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type unitio.c: In function ‘zUnitIOSaveAmberParmFormat_old’: unitio.c:6069: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type unitio.c:6069: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type gcc -c -m64 -DBINTRAJ -o tripos.o tripos.c gcc -c -m64 -DBINTRAJ -o graphUtil.o graphUtil.c graphUtil.c: In function ‘GraphUtilFindAllSmallestRingsAndRingGroups’: graphUtil.c:675: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type graphUtil.c:675: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type gcc -c -m64 -DBINTRAJ -o select.o select.c gcc -c -m64 -DBINTRAJ -o amber.o amber.c amber.c: In function ‘uAmberReadUnitFromPrep’: amber.c:986: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type amber.c:986: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type gcc -c -m64 -DBINTRAJ -o build.o build.c build.c: In function ‘bBuildFlipChiralityFor’: build.c:1901: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type build.c:1901: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type build.c:1907: warning: passing argument 1 of ‘GraphUtilFindAllSmallestRings’ from incompatible pointer type build.c: In function ‘BuildInternalsForSimpleRings’: build.c:2185: warning: passing argument 1 of ‘GraphUtilFindAllSmallestRingsAndRingGroups’ from incompatible pointer type gcc -c -m64 -DBINTRAJ -o elements.o elements.c gcc -c -m64 -DBINTRAJ -o library.o library.c gcc -c -m64 -DBINTRAJ -o chirality.o chirality.c gcc -c -m64 -DBINTRAJ -o minimizer.o minimizer.c gcc -c -m64 -DBINTRAJ -o model.o model.c model.c: In function ‘zModelOrderAtoms’: model.c:497: warning: passing argument 1 of ‘Sift’ from incompatible pointer type gcc -c -m64 -DBINTRAJ -o parmLib.o parmLib.c gcc -c -m64 -DBINTRAJ -o pdbFile.o pdbFile.c pdbFile.c: In function ‘zPdbBuildCoordinatesForContainer’: pdbFile.c:1091: warning: passing argument 1 of ‘BuildFixInternals’ from incompatible pointer type pdbFile.c: In function ‘zPdbAddAtom’: pdbFile.c:1210: warning: passing argument 1 of ‘BuildInternalsForContainer’ from incompatible pointer type pdbFile.c: In function ‘writeTER’: pdbFile.c:1764: warning: initialization from incompatible pointer type gcc -c -m64 -DBINTRAJ -o mol2File.o mol2File.c gcc -c -m64 -DBINTRAJ -o tools.o tools.c tools.c: In function ‘iToolDistanceSearch’: tools.c:1643: warning: passing argument 1 of ‘SortByDouble’ from incompatible pointer type tools.c:1643: warning: passing argument 4 of ‘SortByDouble’ from incompatible pointer type tools.c: In function ‘ToolOrientPrincipleAxisAlongCoordinateAxis’: tools.c:1714: warning: passing argument 2 of ‘MathOpDiagonalize’ from incompatible pointer type gcc -c -m64 -DBINTRAJ -o variables.o variables.c gcc -c -m64 -DBINTRAJ -o parser.o parser.c gcc -c -m64 -DBINTRAJ -o help.o help.c gcc -c -m64 -DBINTRAJ -o utilMakeHelp.o utilMakeHelp.c gcc -o utilMakeHelp basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o utilMakeHelp.o -lm ./utilMakeHelp helptext.text helptext.c gcc -c -m64 -DBINTRAJ -o helptext.o helptext.c gcc -c -m64 -DBINTRAJ -o octree.o octree.c gcc -c -m64 -DBINTRAJ -o commands.o commands.c gcc -c -m64 -DBINTRAJ -o mathop.o mathop.c gcc -c -m64 -DBINTRAJ -o block.o block.c gcc -c -m64 -DBINTRAJ -o restraint.o restraint.c gcc -c -m64 -DBINTRAJ -o hybrid.o hybrid.c gcc -c -m64 -DBINTRAJ -o tLeap.o tLeap.c gcc -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o tLeap.o -lm mv teLeap ../../../../exe make[2]: Leaving directory `/opt/amber10/src/leap/src/leap' Copying shell script sed -e "s?BINDIR?/opt/amber10/bin?" -e "s?DATDIR?/opt/amber10/dat?;" tleap > /opt/amber10/bin/tleap chmod +x /opt/amber10/bin/tleap make skip_xleap make[2]: Entering directory `/opt/amber10/src/leap' NOTE: skipping the building of xleap as X11 libraries are not installed or NOTE: -nox11 was specified as an option to configure. make[2]: Leaving directory `/opt/amber10/src/leap' make[1]: Leaving directory `/opt/amber10/src/leap' (cd gleap && make install ) make[1]: Entering directory `/opt/amber10/src/gleap' cd freelib; make make[2]: Entering directory `/opt/amber10/src/gleap/freelib' cd readline; make make[3]: Entering directory `/opt/amber10/src/gleap/freelib/readline' Makefile:134: warning: overriding commands for target `.c.o' ../../../config.h:99: warning: ignoring old commands for target `.c.o' gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o bind.o bind.c bind.c: In function ‘rl_function_of_keyseq’: bind.c:704: warning: comparison is always true due to limited range of data type gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o callback.o callback.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o compat.o compat.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o complete.o complete.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o display.o display.c display.c: In function ‘rl_character_len’: display.c:1891: warning: comparison is always true due to limited range of data type gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o funmap.o funmap.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o histexpand.o histexpand.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o histfile.o histfile.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o history.o history.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o histsearch.o histsearch.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o input.o input.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o isearch.o isearch.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o keymaps.o keymaps.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o kill.o kill.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o macro.o macro.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o mbutil.o mbutil.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o misc.o misc.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o nls.o nls.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o parens.o parens.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o readline.o readline.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o rltty.o rltty.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o savestring.o savestring.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o search.o search.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o shell.o shell.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o signals.o signals.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o termcap.o termcap.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o terminal.o terminal.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o text.o text.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o tilde.o tilde.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o tparam.o tparam.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o undo.o undo.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o util.o util.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o version.o version.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o vi_mode.o vi_mode.c gcc -c -m64 -DBINTRAJ -DHAVE_CONFIG_H -I. -o xmalloc.o xmalloc.c rm -f libreadline.a ar cqs libreadline.a bind.o callback.o compat.o complete.o display.o funmap.o histexpand.o histfile.o history.o histsearch.o input.o isearch.o keymaps.o kill.o macro.o mbutil.o misc.o nls.o parens.o readline.o rltty.o savestring.o search.o shell.o signals.o termcap.o terminal.o text.o tilde.o tparam.o undo.o util.o version.o vi_mode.o xmalloc.o make[3]: Leaving directory `/opt/amber10/src/gleap/freelib/readline' make[2]: Leaving directory `/opt/amber10/src/gleap/freelib' cd mortsrc; make make[2]: Entering directory `/opt/amber10/src/gleap/mortsrc' cd common;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/common' g++ -c -O2 -Wall -W -D_REENTRANT -I../../freelib -I../../freelib -o numvec.o numvec.cpp numvec.cpp: In function ‘double mort::normal(const mort::numvec&)’: numvec.cpp:124: warning: comparison between signed and unsigned integer expressions numvec.cpp: In function ‘double mort::dot(const mort::numvec&, const mort::numvec&)’: numvec.cpp:159: warning: comparison between signed and unsigned integer expressions numvec.cpp: In function ‘void mort::jacobi(mort::matrix&, mort::numvec&, mort::matrix&, int&)’: numvec.cpp:424: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I../../freelib -I../../freelib -o pertab.o pertab.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I../../freelib -I../../freelib -o fortran.o fortran.cpp fortran.cpp: In member function ‘void mort::format::write(std::ostream&) const’: fortran.cpp:133: warning: comparison between signed and unsigned integer expressions fortran.cpp:138: warning: comparison between signed and unsigned integer expressions fortran.cpp:145: warning: comparison between signed and unsigned integer expressions fortran.cpp:153: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I../../freelib -I../../freelib -o hashcode.o hashcode.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I../../freelib -I../../freelib -o algorithm.o algorithm.cpp rm -f libcommon.a ar cqs libcommon.a numvec.o pertab.o fortran.o hashcode.o algorithm.o make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/common' cd object;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/object' g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o adjacency.o adjacency.cpp adjacency.cpp: In member function ‘bool mort::adjacency_t::empty() const’: adjacency.cpp:86: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o addhs.o addhs.cpp addhs.cpp: In function ‘bool mort::too_close(const std::vector, std::allocator > >&, const mort::numvec&, double)’: addhs.cpp:74: warning: comparison between signed and unsigned integer expressions addhs.cpp: In function ‘void mort::addHs(mort::moref_t&)’: addhs.cpp:203: warning: comparison between signed and unsigned integer expressions addhs.cpp: In function ‘void mort::addHs(mort::molecule_t&)’: addhs.cpp:218: warning: comparison between signed and unsigned integer expressions addhs.cpp:220: warning: comparison between signed and unsigned integer expressions addhs.cpp: In function ‘void mort::addHs(mort::atomvec_t&)’: addhs.cpp:232: warning: comparison between signed and unsigned integer expressions addhs.cpp:237: warning: comparison between signed and unsigned integer expressions addhs.cpp:239: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o atomexpr.o atomexpr.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o atomfun.o atomfun.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o bondfun.o bondfun.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o atomvec.o atomvec.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o component.o component.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o database.o database.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o entity.o entity.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o finder.o finder.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o fixbo.o fixbo.cpp fixbo.cpp:464: warning: unused parameter ‘atms’ g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o molecule.o molecule.cpp molecule.cpp: In member function ‘void mort::molecule_t::remove_atom(const mort::moref_t&)’: molecule.cpp:407: warning: comparison between signed and unsigned integer expressions molecule.cpp:413: warning: comparison between signed and unsigned integer expressions molecule.cpp:419: warning: comparison between signed and unsigned integer expressions molecule.cpp:425: warning: comparison between signed and unsigned integer expressions molecule.cpp:431: warning: comparison between signed and unsigned integer expressions molecule.cpp: In member function ‘void mort::molecule_t::remove_resd(const mort::moref_t&)’: molecule.cpp:460: warning: comparison between signed and unsigned integer expressions molecule.cpp: In function ‘void mort::print_vec(std::ostream&, const std::vector >&)’: molecule.cpp:477: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o molfun.o molfun.cpp molfun.cpp: In function ‘void mort::assign_ring(mort::moref_t&)’: molfun.cpp:83: warning: comparison between signed and unsigned integer expressions molfun.cpp: In function ‘void mort::assign_arom(mort::moref_t&)’: molfun.cpp:139: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o moref.o moref.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o moiter.o moiter.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o namemap.o namemap.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o parmfun.o parmfun.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o resdfun.o resdfun.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o ring.o ring.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I.. -I../../freelib -o subst.o subst.cpp subst.cpp: In member function ‘virtual void mort::subst_finder::list_next(const mort::atomvec_t&, mort::atomvec_t&)’: subst.cpp:81: warning: comparison between signed and unsigned integer expressions make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/object' cd ambfmt;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/ambfmt' g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o ambfrc-amber.o ambfrc-amber.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o ambfrc-amoeba.o ambfrc-amoeba.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o amboff.o amboff.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o chain.o chain.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o exclude.o exclude.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o extent.o extent.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o les.o les.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o parm.o parm.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o parmset.o parmset.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o prep.o prep.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o prmtop-amoeba.o prmtop-amoeba.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o prmtop.o prmtop.cpp prmtop.cpp: In function ‘void mort::prmtop::write_excl_size(const mort::excl_t&, std::ostream&)’: prmtop.cpp:242: warning: comparison between signed and unsigned integer expressions prmtop.cpp: In function ‘void mort::prmtop::write_vdw_index(std::ostream&, int)’: prmtop.cpp:278: warning: comparison between signed and unsigned integer expressions prmtop.cpp: In function ‘void mort::prmtop::write_excl_list(const mort::excl_t&, std::ostream&)’: prmtop.cpp:677: warning: comparison between signed and unsigned integer expressions make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/ambfmt' cd atmask;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/atmask' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o atom.o atom.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o condition.o condition.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o dist.o dist.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o logic.o logic.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o mask.o mask.cpp mask.cpp:37: warning: unused parameter ‘reg’ g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o paren.o paren.cpp paren.cpp:14: warning: unused parameter ‘mol’ g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o resd.o resd.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/atmask' cd capbox;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/capbox' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o addions.o addions.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o octree.o octree.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o shaper.o shaper.cpp shaper.cpp: In member function ‘void mort::capbox::solvent_shaper::make_exclusion_list(double)’: shaper.cpp:67: warning: comparison between signed and unsigned integer expressions shaper.cpp: In member function ‘virtual int mort::capbox::solvent_shaper::check_box(const mort::numvec&, const mort::numvec&, double)’: shaper.cpp:173: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o solvate.o solvate.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/capbox' cd enefrc;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/enefrc' g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o bonding.o bonding.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o ctrlparm.o ctrlparm.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o nonbond-lst.o nonbond-lst.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o nonbond-egb.o nonbond-egb.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o nonbond-pbc.o nonbond-pbc.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/enefrc' cd guilib;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/guilib' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o command.o command.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o console.o console.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o control.o control.cpp control.cpp: In function ‘void mort::interpret(std::string, std::vector, std::allocator >, std::allocator, std::allocator > > >&)’: control.cpp:44: warning: comparison between signed and unsigned integer expressions control.cpp:53: warning: comparison between signed and unsigned integer expressions control.cpp:53: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o grammar.o grammar.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o leaplog.o leaplog.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o mainwin.o mainwin.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/guilib' cd format;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/format' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o ambfrc.o ambfrc.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o amboff.o amboff.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o format.o format.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o mdlfmt.o mdlfmt.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o pdbent.o pdbent.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o prmtop.o prmtop.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o smarts.o smarts.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o tripos.o tripos.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/format' cd smarts;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/smarts' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o parse.o parse.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o reader.o reader.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o status.o status.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/smarts' cd tripos;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/tripos' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o atom.o atom.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o bond.o bond.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o head.o head.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o resd.o resd.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o sect.o sect.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/tripos' cd pdbent;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/pdbent' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o atom.o atom.cpp atom.cpp: In function ‘void mort::pdbent::read_bond(std::istream&, mort::molecule_t&)’: atom.cpp:99: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o build.o build.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o second.o second.cpp make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/pdbent' cd nablib;make make[3]: Entering directory `/opt/amber10/src/gleap/mortsrc/nablib' Makefile:4: warning: overriding commands for target `.c.o' ../../../config.h:99: warning: ignoring old commands for target `.c.o' g++ -c boundsutil.cpp -I../../mortsrc -I../../freelib boundsutil.cpp: In function ‘BOUNDS_T* bsetup(mort::molecule_t&)’: boundsutil.cpp:153: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:153: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:168: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:168: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:195: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:195: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:202: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:202: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:208: warning: deprecated conversion from string constant to ‘char*’ boundsutil.cpp:208: warning: deprecated conversion from string constant to ‘char*’ gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o binpos.o binpos.c gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o conjgrad.o conjgrad.c gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o memutil.o memutil.c g++ -c molsurf.cpp -I../../mortsrc -I../../freelib gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o prm.o prm.c gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o rand2.o rand2.c flex -t mm_options.l | sed -e 's/yy/mmo/g' -e 's/stdout/nabout/' > lex.mm_options.c gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o sff.o sff.c In file included from sff.c:800: mask.c: In function ‘set_belly_mask’: mask.c:72: warning: cast to pointer from integer of different size gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o time.o time.c gcc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ -o traceback.o traceback.c make[3]: Leaving directory `/opt/amber10/src/gleap/mortsrc/nablib' rm -f libmort.a ar cqs libmort.a ambfmt/ambfrc-amber.o ambfmt/ambfrc-amoeba.o ambfmt/amboff.o ambfmt/chain.o ambfmt/exclude.o ambfmt/extent.o ambfmt/les.o ambfmt/parm.o ambfmt/parmset.o ambfmt/prmtop-amoeba.o ambfmt/prmtop.o ambfmt/prep.o atmask/atom.o atmask/condition.o atmask/dist.o atmask/logic.o atmask/mask.o atmask/paren.o atmask/resd.o capbox/addions.o capbox/octree.o capbox/solvate.o capbox/shaper.o common/numvec.o common/pertab.o common/fortran.o common/hashcode.o common/algorithm.o enefrc/bonding.o enefrc/ctrlparm.o enefrc/nonbond-egb.o enefrc/nonbond-lst.o enefrc/nonbond-pbc.o format/ambfrc.o format/amboff.o format/format.o format/mdlfmt.o format/pdbent.o format/prmtop.o format/smarts.o format/tripos.o guilib/command.o guilib/console.o guilib/control.o guilib/mainwin.o guilib/grammar.o guilib/leaplog.o object/adjacency.o object/entity.o object/finder.o object/atomexpr.o object/atomfun.o object/bondfun.o object/atomvec.o object/component.o object/database.o object/moiter.o object/molecule.o object/molfun.o object/parmfun.o object/moref.o object/resdfun.o object/ring.o object/subst.o object/namemap.o object/fixbo.o object/addhs.o pdbent/atom.o pdbent/build.o pdbent/second.o smarts/parse.o smarts/reader.o smarts/status.o tripos/atom.o tripos/bond.o tripos/head.o tripos/resd.o tripos/sect.o nablib/binpos.o nablib/conjgrad.o nablib/memutil.o nablib/prm.o nablib/rand2.o nablib/sff.o nablib/time.o nablib/traceback.o nablib/boundsutil.o nablib/molsurf.o make[2]: Leaving directory `/opt/amber10/src/gleap/mortsrc' cd plugins; make make[2]: Entering directory `/opt/amber10/src/gleap/plugins' g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o add.o add.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o addmap.o addmap.cpp addmap.cpp: In member function ‘virtual bool amber::addmap_command::exec()’: addmap.cpp:35: warning: comparison between signed and unsigned integer expressions addmap.cpp:41: warning: comparison between signed and unsigned integer expressions g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o addions.o addions.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o bond.o bond.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o center.o center.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o charge.o charge.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o copy.o copy.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o create.o create.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o desc.o desc.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o delete.o delete.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o energy.o energy.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o geom.o geom.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o help.o help.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o impose.o impose.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o list.o list.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o loadcrd.o loadcrd.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o loadfrc.o loadfrc.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o loadmol2.o loadmol2.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o loadoff.o loadoff.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o loadpdb.o loadpdb.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o loadprep.o loadprep.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o loadsdf.o loadsdf.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o measure.o measure.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o merge.o merge.cpp g++ -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -c -o moloper.o moloper.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o savemol2.o savemol2.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o saveoff.o saveoff.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o savepdb.o savepdb.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o saveprm.o saveprm.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o savesdf.o savesdf.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o set.o set.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o shell.o shell.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o solvate.o solvate.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o source.o source.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o zmatrix.o zmatrix.cpp rm -f libplugins.a ar cqs libplugins.a add.o addmap.o addions.o bond.o center.o charge.o copy.o create.o desc.o delete.o energy.o geom.o help.o impose.o list.o loadcrd.o loadfrc.o loadmol2.o loadoff.o loadpdb.o loadprep.o loadsdf.o measure.o merge.o moloper.o savemol2.o saveoff.o savepdb.o saveprm.o savesdf.o set.o shell.o solvate.o source.o zmatrix.o make[2]: Leaving directory `/opt/amber10/src/gleap/plugins' cd leapsrc; BINDIR=/opt/amber10/bin make install make[2]: Entering directory `/opt/amber10/src/gleap/leapsrc' g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib -I../plugins -I../freelib -I. -o strmain.o strmain.cpp strmain.cpp:13: warning: unused parameter ‘sig’ g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib -I../plugins -I../freelib -I. -o strbuff.o strbuff.cpp g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib -I../plugins -I../freelib -I. -o plugins.o plugins.cpp g++ -static-libgcc -o sleap strmain.o strbuff.o plugins.o ../freelib/readline/libreadline.a -lm ../plugins/libplugins.a ../mortsrc/libmort.a cp -p sleap /opt/amber10/bin make[2]: Leaving directory `/opt/amber10/src/gleap/leapsrc' make[1]: Leaving directory `/opt/amber10/src/gleap' Completed installation of AmberTools, version 1.1