( cd nab; make test ) make[1]: Entering directory `/home/userid/Documents/amber10/test/nab' ===================================================== Running test to make dna duplex: PASSED ===================================================== Running Reflexive test: PASSED ===================================================== Running test of hashed arrays: PASSED ===================================================== Running test to compute chemical shifts (This tests many parts of the compiler and libraries) PASSED ===================================================== Running test to do simple minimization (This tests the molecular mechanics interface) PASSED ===================================================== Running test to do simple minimization with shake (This tests the molecular mechanics interface) PASSED ===================================================== Running test to do simple minimization (This tests the generalized Born implementation) PASSED ===================================================== Running test to do simple minimization (This tests the LCPO surface area) PASSED ===================================================== Running test to do simple minimization (This tests the ao generalized Born implementation) PASSED ===================================================== Running test to do molecular dynamics with rattle PASSED ===================================================== Running test of fibre-diffraction module PASSED ===================================================== Running test of randomized embedding 1c1 < radius of gyration: 7.340 --- > radius of gyration: 7.294 FAILED (OK if gyration radius is about 7 or 8) ===================================================== Running test to compute NAB energy of 3dfr minus waters. Compare the NAB energy with the previously computed Amber energy: Amber8 total energy is 5184.0880 NAB total energy is 5184.0880 PASSED ===================================================== Running test to create Amber force-field description PASSED ===================================================== checking the prmtop file: PASSED ===================================================== Running test to compute GB Newton-Raphson and normal modes: PASSED ===================================================== Running test to compute non-GB Newton-Raphson and normal modes: PASSED ===================================================== Running test to create a simple mmCIF file PASSED ===================================================== Running test to do simple xmin minimization PASSED ===================================================== Running test to compute GB normal modes using DSYEVD: PASSED ===================================================== Running test to compute GB normal modes using DSAUPD: PASSED ===================================================== Running test to compute Langevin modes: PASSED ===================================================== Running test to do simple lmod optimization 1c1 < Glob. min. E = -122.793 kcal/mol --- > Glob. min. E = -122.191 kcal/mol FAILED (probably OK if energy is -115 to -125) ===================================================== Running test to do simple minimization (This tests the generalized Born implementation) PASSED ===================================================== make[1]: Leaving directory `/home/userid/Documents/amber10/test/nab' cd ptraj_rmsa && ./Run.rms diffing rms.dat.save with rms.dat PASSED ============================================================== cd ptraj_rms && ./Run.rms ptraj: test rms and 2drms commands diffing rms_fit.dat.save with rms_fit.dat PASSED ============================================================== diffing rms_nofit.dat.save with rms_nofit.dat PASSED ============================================================== diffing rms2d.ps.save with rms2d.ps PASSED ============================================================== cd ptraj_matrix && ./Run.matrix ptraj: analyze fluctuation matrices diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat PASSED ============================================================== diffing 1rrb_vac_mwcovarmat_evecs.dat.save with 1rrb_vac_mwcovarmat_evecs.dat PASSED ============================================================== diffing 1rrb_vac_distcovarmat_evecs.dat.save with 1rrb_vac_distcovarmat_evecs.dat PASSED ============================================================== cd antechamber/top2mol2 && ./Run.top2mol2 diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing dna.mol2.save with dna.mol2 PASSED ============================================================== diffing dna_wat.mol2.save with dna_wat.mol2 PASSED ============================================================== diffing aa.mol2.save with aa.mol2 PASSED ============================================================== cd antechamber/database && ./Run.database diffing total.frcmod.save with total.frcmod PASSED ============================================================== diffing total.prepi.save with total.prepi PASSED ============================================================== cd antechamber/bondtype && ./Run.bondtype diffing ABAKOE.prepi.save with ABAKOE.prepi PASSED ============================================================== diffing PFPHHG02.prepi.save with PFPHHG02.prepi PASSED ============================================================== diffing fluorescein2.mol2.save with fluorescein2.mol2 PASSED ============================================================== diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2 PASSED ============================================================== cd antechamber/c60 && ./Run.c60 diffing buckyball.mol2.save with buckyball.mol2 PASSED ============================================================== diffing buckyball.gzmat.save with buckyball.gzmat PASSED ============================================================== diffing buckyball.jcrt.save with buckyball.jcrt PASSED ============================================================== diffing buckyball.prepi.save with buckyball.prepi PASSED ============================================================== diffing buckyball.ac.save with buckyball.ac PASSED ============================================================== cd antechamber/charmm && ./Run.charmm diffing ala2.inp.save with ala2.inp PASSED ============================================================== diffing ala2.rtf.save with ala2.rtf PASSED ============================================================== diffing ala2.prm.save with ala2.prm possible FAILURE: check ala2.prm.dif ============================================================== diffing ala2_charmm.mol2.save with ala2_charmm.mol2 PASSED ============================================================== cd antechamber/chemokine && ./Run.1b2t diffing 1b2t.mol2.save with 1b2t.mol2 PASSED ============================================================== diffing 1b2t.ac.save with 1b2t.ac PASSED ============================================================== cd antechamber/tp && ./Run.tp diffing tp.mol2.save with tp.mol2 possible FAILURE: check tp.mol2.dif ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/ash && ./Run.ash diffing ash.mol2.save with ash.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/sustiva && ./Run.sustiva diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out PASSED ============================================================== cd antechamber/fluorescein && ./Run.fluorescein diffing fluorescein.mol2.save with fluorescein.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/guanine_amber && ./Run.guanine_amber diffing DGN.mol2.save with DGN.mol2 possible FAILURE: check DGN.mol2.dif ============================================================== cd antechamber/fpph && ./Run.fpph_resp diffing fpph_resp.mol2.save with fpph_resp.mol2 PASSED ============================================================== cd antechamber/residuegen && ./Run.ala diffing ala.ac.save with ala.ac PASSED ============================================================== diffing ala.esp.save with ala.esp PASSED ============================================================== diffing ala.prep.save with ala.prep PASSED ============================================================== (cd leap && ./Run.tleap) AMBERHOME is set to /home/userid/Documents/amber10 Running leap tests on ./tleap -> ../../exe/teLeap building force field libraries: '91 ff.. diffing ../../dat/leap/lib/all_amino91.lib with all_amino91.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminont91.lib with all_aminont91.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib PASSED ============================================================== diffing ../../dat/leap/lib/ions91.lib with ions91.lib PASSED ============================================================== '94 ff.. diffing ../../dat/leap/lib/all_amino94.lib with all_amino94.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminont94.lib with all_aminont94.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib PASSED ============================================================== diffing ../../dat/leap/lib/ions94.lib with ions94.lib PASSED ============================================================== loadpdb and saveamberparm: 94 ff.. - aminoan94 comparing topology to earlier leap version.. diffing ff94/all_aminoan94.top with all_aminoan94.top PASSED ============================================================== No /home/userid/Documents/amber10/exe/sander to use to compare energies - aminonc94 comparing topology to earlier leap version.. diffing ff94/all_aminonc94.top with all_aminonc94.top PASSED ============================================================== No /home/userid/Documents/amber10/exe/sander to use to compare energies - dna94 comparing topology to earlier leap version.. diffing ff94/all_dna94.top with all_dna94.top PASSED ============================================================== No /home/userid/Documents/amber10/exe/sander to use to compare energies - rna94 comparing topology to earlier leap version.. diffing ff94/all_rna94.top with all_rna94.top PASSED ============================================================== No /home/userid/Documents/amber10/exe/sander to use to compare energies -------------------------------------------------------------- Notes: - If all tests PASSED, you can 'rm *.log *.out *.lib *.top' - For a discussion of energy differences (sander*.dif) see 0README. - It is common to see round-off differences in the portion of these tests -------------------------------------------------------------- (cd sleap && make test ) make[1]: Entering directory `/home/userid/Documents/amber10/test/sleap' rm -f `find . -name "*.dif"` rm -f TEST_FAILURES.diff cd mdlsdf; ./Run.mdlsdf /bin/rm: cannot remove `crown_2.sdf': No such file or directory diffing crown_2.sdf.save with crown_2.sdf PASSED ============================================================== cd tripos; ./Run.tripos diffing wy.mol2.save with wy.mol2 PASSED ============================================================== cd pdbent; ./Run.pdbent diffing 1hpv.mol2.save with 1hpv.mol2 PASSED ============================================================== cd pdbent; ./Run.pdbent2 diffing mdl_1hpv.mol2.save with mdl_1hpv.mol2 PASSED ============================================================== cd offlib; ./Run.off diffing hpv.off.save with hpv.off PASSED ============================================================== cd source; ./Run.source diffing source.out.save with source.out PASSED ============================================================== cd prmtop; ./Run.prmtop1 diffing hpv.top.save with hpv.top PASSED ============================================================== diffing hpv.xyz.save with hpv.xyz PASSED ============================================================== cd prmtop; ./Run.prmtop2 this is long test, wait patiently..... diffing box.out.save with box.out PASSED ============================================================== diffing hpv_box.top.save with hpv_box.top PASSED ============================================================== cd prmtop; ./Run.prmtop3 this is a long test, wait patiently... diffing hpv_cap.top.save with hpv_cap.top PASSED ============================================================== cd prmtop; ./Run.prmtoppol diffing ubqpol.top.save with ubqpol.top PASSED ============================================================== diffing ubqpol.xyz.save with ubqpol.xyz PASSED ============================================================== cd solvate; ./Run.solvatebox long test, wait patiently... diffing hpvbox.pdb.save with hpvbox.pdb PASSED ============================================================== diffing hpvbox.top.save with hpvbox.top PASSED ============================================================== cd solvate; ./Run.solvatebox_closeness long test, wait patiently... diffing hpvbox_closeness.pdb.save with hpvbox_closeness.pdb PASSED ============================================================== cd solvate; ./Run.solvatecap diffing hpvcap.pdb.save with hpvcap.pdb PASSED ============================================================== cd solvate; ./Run.solvateoct long test, wait patiently... diffing hpvoct.pdb.save with hpvoct.pdb PASSED ============================================================== cd solvate; ./Run.solvateshell long test, wait patiently... diffing hpvshell.pdb.save with hpvshell.pdb PASSED ============================================================== cd amoeba; ./Run.amoeba diffing jac_2.prmtop.save with jac_2.prmtop PASSED ============================================================== cd amoeba; ./Run.amoeba_sol diffing hpv.prmtop.save with hpv.prmtop PASSED ============================================================== cd builder; ./Run.builder diffing water.mol2.save with water.mol2 PASSED ============================================================== diffing wat2.mol2.save with wat2.mol2 PASSED ============================================================== cd addions; ./Run.addions diffing hpv_ion.pdb.save with hpv_ion.pdb PASSED ============================================================== cd molinfo; ./Run.molinfo diffing leap.out.save with leap.out PASSED ============================================================== cd polymer; ./Run.polymer rm: cannot remove `combine.mol2': No such file or directory rm: cannot remove `sequence.mol2': No such file or directory diffing combine.mol2.save with combine.mol2 PASSED ============================================================== diffing sequence.mol2.save with sequence.mol2 PASSED ============================================================== cd polymer; ./Run.impose rm: cannot remove `impose.out': No such file or directory rm: cannot remove `impose.mol2': No such file or directory diffing impose.out.save with impose.out PASSED ============================================================== diffing impose.mol2.save with impose.mol2 PASSED ============================================================== cd polymer; ./Run.polymer2 rm: cannot remove `aa.mol2': No such file or directory diffing aa.mol2.save with aa.mol2 PASSED ============================================================== cd polymer; ./Run.zmatrix rm: cannot remove `zmatrix.out': No such file or directory rm: cannot remove `meoh.mol2': No such file or directory diffing zmatrix.out.save with zmatrix.out PASSED ============================================================== diffing meoh.mol2.save with meoh.mol2 PASSED ============================================================== cd bondbydis; ./Run.bondbydis rm: cannot remove `wy.sdf': No such file or directory diffing wy.sdf.save with wy.sdf PASSED ============================================================== cd DNA; ./Run.DNA1 diffing 132d.mol2.save with 132d.mol2 PASSED ============================================================== cd DNA; ./Run.DNA2 diffing 32d.top.save with 32d.top PASSED ============================================================== cd oldleap; ./Run.oldleap diffing ff91/all_amino91.lib.save with ff91/all_amino91.lib PASSED ============================================================== diffing ff91/all_aminont91.lib.save with ff91/all_aminont91.lib PASSED ============================================================== diffing ff91/all_aminoct91.lib.save with ff91/all_aminoct91.lib PASSED ============================================================== diffing ff91/all_nucleic91.lib.save with ff91/all_nucleic91.lib PASSED ============================================================== diffing ff94/all_amino94.lib.save with ff94/all_amino94.lib PASSED ============================================================== diffing ff94/all_aminont94.lib.save with ff94/all_aminont94.lib PASSED ============================================================== diffing ff94/all_aminoct94.lib.save with ff94/all_aminoct94.lib PASSED ============================================================== diffing ff94/all_nucleic94.lib.save with ff94/all_nucleic94.lib PASSED ============================================================== diffing ff94/all_aminoan94.top.save with ff94/all_aminoan94.top PASSED ============================================================== diffing ff94/all_aminoan94.crd.save with ff94/all_aminoan94.crd PASSED ============================================================== diffing ff94/all_aminonc94.top.save with ff94/all_aminonc94.top PASSED ============================================================== diffing ff94/all_aminonc94.crd.save with ff94/all_aminonc94.crd PASSED ============================================================== diffing ff94/all_dna94.top.save with ff94/all_dna94.top PASSED ============================================================== diffing ff94/all_dna94.crd.save with ff94/all_dna94.crd PASSED ============================================================== diffing ff94/all_rna94.top.save with ff94/all_rna94.top PASSED ============================================================== diffing ff94/all_rna94.crd.save with ff94/all_rna94.crd PASSED ============================================================== cd disulfide; ./Run.auto diffing crn.mol2.save with crn.mol2 PASSED ============================================================== cd disulfide; ./Run.manu diffing crn.mol2.save with crn.mol2 PASSED ============================================================== cd disulfide; ./Run.auto.H diffing crn.H.mol2.save with crn.H.mol2 PASSED ============================================================== diffing crn.top.save with crn.top PASSED ============================================================== diffing crn.xyz.save with crn.xyz PASSED ============================================================== make[1]: Leaving directory `/home/userid/Documents/amber10/test/sleap' (cd resp && ./Run.ade ) RESP stage 1: diffing ade_1st.out.save with ade_1st.out PASSED ============================================================== diffing ade_1st.pch.save with ade_1st.pch PASSED ============================================================== diffing ade_1st_calc.esp.save with ade_1st_calc.esp PASSED ============================================================== RESP stage 2: diffing ade_1st.chg.save with ade_1st.chg PASSED ============================================================== diffing ade_2nd.out.save with ade_2nd.out PASSED ============================================================== diffing ade_2nd.pch.save with ade_2nd.pch PASSED ============================================================== diffing ade_2nd.chg.save with ade_2nd.chg PASSED ============================================================== (cd reduce && ./Run.reduce ) diffing 1ubqH.pdb.save with 1ubqH.pdb PASSED ============================================================== Finished test suite for AmberTools