Category: structural dna nanotechnology

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A NanoEngineer-1 Note (DNA Conversion Site, Recent Article, Related Links)

Above: A six-stranded triple-crossover (TX) DNA Junction. See Ned Seeman's ACS interview for more background.

Having just mentioned it in the context of making publication-quality pretty pictures, another brief note thanks to a citation request on the NanoEngineer Development/User Group (groups.google.com/group/nanoengineer-dev).

There's a website hosted at bionano.physics.illinois.edu for the conversion of NE-1 DNA mmp files to all-atom pdb ("Molecular Dynamics Simulation of Custom DNA Nanostructures Created by NanoEngineer-1") and NE-1's FNANO08 proceedings article ("NanoEngineer-1 – A CAD-based molecular modeling program for structural DNA nanotechnology") was included (with thanks to its use by German Barcenas) in the recent International Journal Of Molecular Sciences article "Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions."

The bionano site is a dramatic improvement from the NAMOT + sed'ing I worked up many years ago while getting something DNA-related stood up.

As a still-not-irregular user myself, I can appreciate the small hurdles needed to keep the program upright in modern OSs (or the need to just run VirtualBox and be done with it) – therefore noting both Bryan Bishop's dev page (worth the visit to github for the preserved gallery alone!) and Bruce Allen's Molecular Dynamics Studio effort and sourceforge-available download.

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3Dmol.js And WordPress – A Few Simple Worked Examples

A short post describing how to get 3Dmol.js doing something practical in WordPress, hopefully sparing someone else some mild confusion and error messages. In retrospect, the setup is trivial and works beautifully – it's an excellent tool for bringing small molecules, proteins, nanostructures, and others to life with a loading time on-par with how long it takes pages on this site to load generally.

Custom HTML

All of the 3Dmol.js content goes into Custom HTML blocks. You can have as many of the "div" as you like in the same block or have them all separate. Place the script (below) above them all.

script

Into your first Custom HTML block, place the following:

<script src="https://3Dmol.org/build/3Dmol-min.js"></script>

div (and comments)

I'm using 2NA5, my co-authored contribution to the RCSB Protein Data Bank (or at proteopedia), as the example for some of the peptide visualization capabilities. The breakdown by section that renders the structure you see is as follows:

<div style=
"height: 550px; 
width: 550px; 
margin: 20px 0px 20px 0px;
position: relative;"

Defining viewer size and placement, with the specific 550px width here for the WordPress Twenty Seventeen theme I'm still using on this site (else go the full 1000px if you're doing a single-column page with the same theme). The "margin" here is to provide some space between the rendering window and any text above or below it.

class="viewer_3Dmoljs"

Direct from the Bioinformatics article: "HTML authors do not need to use JavaScript to embed 3D viewers within their websites. 3Dmol.js will automatically turn any HTML element annotated with the viewer_3Dmoljs class into a viewer."

data-pdb="2NA5"
data-href="/structures/2NA5.pdb"

If you're loading directly from the PDB, use data-pdb. If storing locally (or somewhere with a specific location), data-href and the directory structure off the main site is all you need. I've gone ahead and made a www.somewhereville.com/structures folder in my WordPress instance to keep .pdb and .mol2 files localized (hence the data-href above), else you can call directly from the link you're provided when you upload them to your site.

data-backgroundcolor="0xeeeeee"

An almost-white background (instead of pure 0xffffff) to easily see the placement of the viewer for this example (and back to white backgrounds for the other structures below).

data-style1="stick:radius=0.1"
data-style2="sphere:radius=0.3"
data-style3="cartoon:color=spectrum"

The business-end of the rendering. This structure has three different data-style representations, for which you need to have a -style1 (here, thinned sticks), -style2 (here, scaled vdW spheres), -style3 (here, peptide backbone cartoon) to call them and to make your custom tweaks to the rendering (after the colons). If you're only going to use one data-style, you can skip the numbering. The "spectrum" style here for the cartoon applies a rainbow gradient to the backbone.

data-surface='opacity:.7;color:spectrum'

The surface styles work like the data styles. Note the colons and semicolons in changing the rendering. Here, the "spectrum" call for the data-surface provides the by-atom coloration on the surface as shown.

data-ui="true">
</div>

Show the controls so the user can play with the structure, close up the div, and that's it. The final block as one piece (for ease of copying + pasting) looks like the following:

<script src="https://3Dmol.org/build/3Dmol-min.js"></script>
<div style="height: 550px; width: 550px; margin: 20px 0px 20px 0px" class="viewer_3Dmoljs" data-pdb="2NA5" data-backgroundcolor="0xeeeeee" data-style1="stick:radius=0.1" data-style2="sphere:radius=0.3" data-style3="cartoon:color=spectrum" data-surface='opacity:.7;color:spectrum' data-ui="true"></div>

And the over-stylized results for 2NA5 is shown below:

Controls

To anyone wanting to drive the structure above or items below, these are the operations from the 3Dmol tutorial page (3dmol.org/doc/tutorial-url.html).

MovementMouse InputTouch Input
RotationPrimary Mouse ButtonSingle touch
TranslationMiddle Mouse Button or Ctrl+PrimaryTriple touch
ZoomScroll Wheel or Second Mouse Button or Shift+PrimaryPinch (double touch)
SlabCtrl+SecondNot Available

pdb and mol2

You will note that no hydrogen atoms are shown for the PDB 2NA5 file above (or any other .pdb file), nor are the H atoms shown for the crimp junction structure from the nano gallery shown below:

While one can play games in the .pdb file to show atoms where the H atoms are in the structure, a simple alternative is to convert the .pdb into a .mol2 with something like openbabel (how I did the conversion as shown below), after which all atoms are now represented:

… and also with a data-surface call added for show (which is to say, the surface is generated for the structure, not from anything PDB-specific).

And, to close up this first quick guide, a reproduction of the TX junction from the nano gallery is provided, with the div block to produce the six distinct chain colors and renderings as shown below:

<div style="height: 550px; width: 550px;  margin: 20px 0px 20px 0px; position: relative;" class="viewer_3Dmoljs" data-href="/structures/TX_DNA.pdb" data-backgroundcolor="0xffffff" 
data-select1='chain:A' 
data-surface1='opacity:.9;color:red' 
data-style1='stick:color=red'
data-select2='chain:B' 
data-surface2='opacity:.9;color:deepskyblue' 
data-style2='stick:color=deepskyblue'
data-select3='chain:C' 
data-surface3='opacity:.3;color:brown' 
data-style3='stick:color=brown'
data-select4='chain:D' 
data-surface4='opacity:.3;color:orange' 
data-style4='stick:color=orange'
data-select5='chain:E' 
data-surface5='opacity:.3;color:green' 
data-style5='stick:color=green'
data-select6='chain:F' 
data-surface6='opacity:.3;color:purple' 
data-style6='stick:color=purple'
data-ui="true"></div>

And give it a few seconds to throw the surfaces up.

Relevant links:

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NAMOT Pre-Release 2.2.0-pre4 In OSX 10.8 (Maybe Older Versions)

A recent visit to the College of Nanoscale Science and Engineering (CNSE) at SUNY Albany inspired a few new DNA ideas that I decided would be greatly simplified by having NAMOT available again for design. Having failed at the base install of the NAMOT 2 version and, unfortunately, not having NAMOT available in Fink for a simple installation, the solution became to build the pre-release from scratch. Ignoring the many errors one encounters while walking through an OSX/Xcode/Fink/X11 bootstrap, the final procedure worked well and without major problem. As usual, the error messages at varied steps are provided below because, I assume, those messages are what you're searching for when you find your way here.

0. Required Installations

You'll need the following installed for this particular build. I believe XCode is the only thing that you'll have to pay for (if you don't already have it. I seem to remember paying $5 through the App Store).

1. XCode

The OSX Developer Suite – developer.apple.com/xcode

2. XQuartz

An OSX (X.Org) X Window System – xquartz.macosforge.org/landing/

3. Fink

An OSX port program for a host of Unix codes and libraries – www.finkproject.org

3a. GSL

The GNU Scientific (C and C++) Libraries – www.gnu.org/software/gsl. This will be installed with Fink.

3b. LessTif

An OSF/Motif clone (made available for OSX through Fink) – lesstif.sourceforge.net. This will be installed with Fink.

4. NAMOT2.2.0-pre4

The -pre4 is currently available (from 2003) from sourceforge.net/projects/namot/files/. I did not try -pre3 and had no luck with the official 2 release.

And, with that…

1. XCode

Blindly follow the install procedure. Several steps below deal with working around the default install locations (specifically, /sw).

2. XQuartz

If you don't have XQuartz installed, you're configure step…

cd Downloads
cd namot-2.2.0-pre4
./configure

will produce the following error…

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
creating libtool
checking for X... no
checking for main in -lX11... no
NAMOT requires Xwindows

Blindly follow the XQuartz install process. After the installations, you'll receive the same error as above. The –x-libraries= and –x-includes= additions to configure below direct the script to the proper libraries and includes.

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

Hopefully, you'll find yourself past the first install problem and onto the second problem.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
creating libtool
checking for X... libraries /usr/X11/lib/, headers /usrX11/include/
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... no
NAMOT requires GNU Scientific Library

3. Fink

The next two codes that need to be installed are the GNU Scientific Libraries and LessTif, both of which are much easier to install using Fink. It is generally useful for many other codes as well, so a good program for any computational chemist to have on hand. The install should be non-problematic despite having to build it from source in 10.6 – 10.8 (as of January 2013). If you build with all the default settings, you'll have no trouble after.

cd Downloads
cd fink-0.34.4
./bootstrap

I chose the default settings throughout.

Fink must be installed and run with superuser (root) privileges. Fink can automatically try to become root when it's run from a user account. Since you're currently running this script as a normal user, the method you choose will also be used immediately for this script. Available methods:

(1)	Use sudo
(2)	Use su
(3)	None, fink must be run as root

Choose a method: [1] 

...

You should now have a working Fink installation in '/sw'. You still need package descriptions if you want to compile packages yourself. You can get them by running either of the commands: 'fink selfupdate-rsync', to update via rsync (generally preferred); or 'fink selfupdate-cvs', to update via CVS (more likely to work through a firewall).

Run '. /sw/bin/init.sh' to set up this terminal session environment to use Fink. To make the software installed by Fink available in all of your future terminal shells, add '. /sw/bin/init.sh' to the init script '.profile' or '.bash_profile' in your home directory. The program /sw/bin/pathsetup.sh can help with this. Enjoy.

Then you run the final step in Fink below:

/sw/bin/pathsetup.sh

Which will produce the following two pop-ups notifying you of shell modifications.

3a. GSL

With the install of Fink, you need to install GSL and LessTif. If you try to install either immediately after installation…

fink install gsl

…you'll receive the following error:

Password:
Scanning package description files..........
Information about 305 packages read in 0 seconds.
no package found for "gsl"
Failed: no package found for specification 'gsl'!

Required after the installation is a fink selfupdate.

fink selfupdate

As usual, follow the default settings…

fink needs you to choose a SelfUpdateMethod.

(1)	cvs
(2)	Stick to point releases
(3)	rsync

Choose an update method [3] 
/usr/bin/find /sw/fink -name CVS -type d -print0 | xargs -0 /bin/rm -rf
fink is setting your default update method to rsync
...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/base/base-files_1.9.13-1_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/base/fink-mirrors_0.34.4.1-1_darwin-i386.deb

Which then leads to a successful GSL install.

fink install gsl

Producing the following output…

Information about 12051 packages read in 1 seconds.
The package 'gsl' will be built and installed.
Reading build dependency for gsl-1.15-1...
Reading dependency for gsl-1.15-1...
Reading runtime dependency for gsl-1.15-1...
Reading dependency for gsl-shlibs-1.15-1...
...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/sci/gsl-shlibs_1.15-1_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/sci/gsl_1.15-1_darwin-i386.deb

Attempting a fresh build after the GSL step…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

…then still produces the following error:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... no
NAMOT requires GNU Scientific Library

As mentioned above, there are a few redirects that need to be made after the XCode / Fink install to put libraries and includes where, in this case, NAMOT expects them. To perform this task, we'll be using symbolic links.

sudo ln -s /sw/include/gsl /usr/include/
sudo ln -s /sw/lib/libgsl* /usr/lib

Now attempting a build…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include

Gets you past the GSL issue.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... yes
checking for main in -lgsl... yes
checking for XShmCreateImage in -lXext... yes
checking for main in -lXt... yes
checking for main in -lXm... no
NAMOT requires Motif...try LessTif(http://www.lesstif.org)

3b. LessTif

The LessTif symbolic links work the same as the GSL symbolic links. This fink install may take a while.

fink install lesstif

Output below…

Information about 12051 packages read in 1 seconds.
The package 'lesstif' will be built and installed.
Reading build dependency for lesstif-0.95.2-4...
Reading dependency for lesstif-0.95.2-4...
Reading runtime dependency for lesstif-0.95.2-4...
...
Setting up lesstif (0.95.2-4) ...
Clearing dependency_libs of .la files being installed

Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/x11/app-defaults_20010814-12_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif-bin_0.95.2-4_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif-shlibs_0.95.2-4_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif_0.95.2-4_darwin-i386.deb

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

But, unfortunately, the LessTif libraries are not in the expected locations.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... yes
checking for main in -lgsl... yes
checking for XShmCreateImage in -lXext... yes
checking for main in -lXt... yes
checking for main in -lXm... no
NAMOT requires Motif...try LessTif(http://www.lesstif.org)

So we add the symbolic links…

sudo ln -s /sw/lib/libXm.* /usr/lib
sudo ln -s /sw/include/Xm /usr/include

Which, finally, runs configure…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

…with no errors.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
config.status: creating docs/demos/curve/Makefile
config.status: creating docs/demos/dit/Makefile
config.status: creating docs/demos/Makefile
config.status: creating config.h
config.status: executing depfiles commands

NOTE: The make step with Python 2.6 produces the following error below. I did not diagnose this beyond the failure to build under 10.6. OSX 10.8 comes with Python 2.7, which did not produce this problem (I'm assuming this is the origin of the problem).

make

…will produce the following error at the pngwriter.c step.

/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..    -DLIB_HOME="\"/usr/local/share/namot\"" -DHELP_FILE_DIR="\"/usr/local/share/namot\"" -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/config -g -O2 -c -o _pynamot_la-pngwriter.lo `test -f 'pngwriter.c' || echo './'`pngwriter.c
gcc -DHAVE_CONFIG_H -I. -I. -I.. -DLIB_HOME=\"/usr/local/share/namot\" -DHELP_FILE_DIR=\"/usr/local/share/namot\" -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/config -g -O2 -c pngwriter.c -MT _pynamot_la-pngwriter.lo -MD -MP -MF .deps/_pynamot_la-pngwriter.TPlo  -fno-common -DPIC -o _pynamot_la-pngwriter.lo
pngwriter.c: In function 'dump_PNG':
pngwriter.c:28: error: 'png_structp' undeclared (first use in this function)
pngwriter.c:28: error: (Each undeclared identifier is reported only once
pngwriter.c:28: error: for each function it appears in.)
pngwriter.c:28: error: expected ';' before 'png_ptr'
pngwriter.c:29: error: 'png_infop' undeclared (first use in this function)
pngwriter.c:29: error: expected ';' before 'info_ptr'
pngwriter.c:30: error: 'png_byte' undeclared (first use in this function)
pngwriter.c:30: error: 'row_pointers' undeclared (first use in this function)
pngwriter.c:30: error: expected expression before ')' token
pngwriter.c:31: error: 'png_text' undeclared (first use in this function)
pngwriter.c:31: error: expected ';' before 'text_ptr'
pngwriter.c:39: warning: incompatible implicit declaration of built-in function 'memset'
pngwriter.c:39: error: 'text_ptr' undeclared (first use in this function)
pngwriter.c:47: error: 'png_ptr' undeclared (first use in this function)
pngwriter.c:47: error: 'PNG_LIBPNG_VER_STRING' undeclared (first use in this function)
pngwriter.c:48: error: 'png_voidp' undeclared (first use in this function)
pngwriter.c:57: error: 'info_ptr' undeclared (first use in this function)
pngwriter.c:60: error: 'png_infopp' undeclared (first use in this function)
pngwriter.c:82: error: 'PNG_COLOR_TYPE_RGB' undeclared (first use in this function)
pngwriter.c:82: error: 'PNG_INTERLACE_ADAM7' undeclared (first use in this function)
pngwriter.c:83: error: 'PNG_COMPRESSION_TYPE_DEFAULT' undeclared (first use in this function)
pngwriter.c:83: error: 'PNG_FILTER_TYPE_DEFAULT' undeclared (first use in this function)
pngwriter.c:85: error: 'PNG_sRGB_INTENT_ABSOLUTE' undeclared (first use in this function)
pngwriter.c:90: error: 'PNG_TEXT_COMPRESSION_NONE' undeclared (first use in this function)
pngwriter.c:93: error: 'PNG_TEXT_COMPRESSION_zTXt' undeclared (first use in this function)
pngwriter.c:104: error: expected expression before ')' token
make[2]: *** [_pynamot_la-pngwriter.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

The build on 10.8 continues as below, with a few warnings about the symbolic link usage that do not seem to affect the program usability (or continued build).

make

Results below…

make  all-recursive
Making all in src
source='namot_wrap.c' object='_pynamot_la-namot_wrap.lo' libtool=yes \
	depfile='.deps/_pynamot_la-namot_wrap.Plo' tmpdepfile='.deps/_pynamot_la-namot_wrap.TPlo' \
	depmode=gcc3 /bin/sh ../depcomp \
	/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..    -DLIB_HOME="\"/usr/local/share/namot\"" -DHELP_FILE_DIR="\"/usr/local/share/namot\"" -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config -g -O2 -c -o _pynamot_la-namot_wrap.lo `test -f 'namot_wrap.c' || echo './'`namot_wrap.c

...

*** Warning: linker path does not have real file for library -lXm.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libXm and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libXm.la

*** Warning: linker path does not have real file for library -lgsl.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libgsl and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libgsl.la

*** Warning: linker path does not have real file for library -lgslcblas.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libgslcblas and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libgslcblas.la

*** Warning: libtool could not satisfy all declared inter-library
*** dependencies of module _pynamot.  Therefore, libtool will create
*** a static module, that should work as long as the dlopening
*** application is linked with the -dlopen flag.

...

Making all in libs
make[2]: Nothing to be done for `all'.
Making all in docs
Making all in helpfiles
make[3]: Nothing to be done for `all'.
Making all in demos
Making all in 6way
make[4]: Nothing to be done for `all'.
Making all in bending
make[4]: Nothing to be done for `all'.
Making all in cube
make[4]: Nothing to be done for `all'.
Making all in curve
make[4]: Nothing to be done for `all'.
Making all in dit
make[4]: Nothing to be done for `all'.
make[4]: Nothing to be done for `all-am'.
make[3]: Nothing to be done for `all-am'.
Making all in etc
make[2]: Nothing to be done for `all'.

Finally, the install…

make install

Which produces the following:

Making install in src
/bin/sh ../mkinstalldirs /usr/local/lib
 /bin/sh ../libtool --mode=install /usr/bin/install -c  _pynamot.la /usr/local/lib/_pynamot.la
/usr/bin/install -c .libs/_pynamot.lai /usr/local/lib/_pynamot.la
/usr/bin/install -c .libs/_pynamot.a /usr/local/lib/_pynamot.a
ranlib /usr/local/lib/_pynamot.a
chmod 644 /usr/local/lib/_pynamot.a
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/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 `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
...
/bin/sh ../mkinstalldirs /usr/local/share/namot
 /usr/bin/install -c -m 644 Namot2.512 /usr/local/share/namot/Namot2.512
 /usr/bin/install -c -m 644 Namot2.600 /usr/local/share/namot/Namot2.600
 /usr/bin/install -c -m 644 Namot2.700 /usr/local/share/namot/Namot2.700
 /usr/bin/install -c -m 644 icon1.xv /usr/local/share/namot/icon1.xv
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.

With luck, your launching of NAMOT will open XQuartz and produce a fully operational NAMOT session.

namot

And, for more assistance with producing DNA files for GROMACS, consider the Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-NAMOT-GROMACS v1, sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS Topology Generation v1, and sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To ffAMBER Format For GROMACS Topology Generation v1 pages on this blog.