VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jun 13 2018 - 09:10:27 CDT

Hi Francesco,

Coordinates are easy. They are passed along with the -c option to grompp. Velocities... Probably its possible somehow once you convert the file types. The difficulty is going to be that the tpr file that grompp generates normally doesn't (and maybe cannot?) include velocities. Instead, input velocities are normally passed directly to mdrun, so that is something outside of the TopoGromacs pipeline. FEP specification is also not covered by TopoGromacs. In GROMACS, FEP is specified at the level of the topology file. I didn't want to deal with it when I was writing TopoGromacs, and my own use cases were all equilibrium simulations anyway, so you may need to edit the code to correctly handle FEP.

-Josh

On 2018-06-13 07:42:30-06:00 Francesco Pietra wrote:

Hi Joshua: Following your indications and a preliminary reading of your paper, I applied topogromacs to my charmm36-parameterized system of a protein with GDP ligand and a diterpenoid ligand (the latter defined in a .str streaming file, without the need of a separate .a prm file) getting the .top file with apparently all components. A most astonishing conversion!

I am still unfamiliar with GROMACS (planning to use it to compare FEP simulations with NAMD) but may I boldly ask whether passing .the .top file to grompp there is a way to preserve the velocities, or at least the equilibrated coordinates, of NAMD?

Thanks a lot, also to John

francesco

On Wed, Jun 13, 2018 at 11:53 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
Yup, as John described, normally a user does NOT need to change anything in this folder if they are running a 1.9.4 alpha or 1.9.2. The regular workflow works where you load your namd psf file, and then execute the commands described in the paper (10.1021/acs.jcim.6b00103):

package require topotools
topo writegmxtop <outputname>.top [list prmfile1.prm prmfile2.prm ...]

When running on 1.9.3, you may need to fix a syntax error that was introduced right before release in the acknowledgements in the directory John specified (see http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28199.html).<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fmailing_list%2Fvmd-l%2F28199.html).&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cf487d9a59cc24043c77008d5d13380a1%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636644941505503301&sdata=i3E2OJ4EPGeTfzy7l4M18KKc1%2FalVLNHVSVnc84bsvc%3D&reserved=0>

-Josh

On 2018-06-11 15:36:21-06:00 owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> wrote:

Hi,
  If you look in the VMD installation folder, you'll see that the topogromacs
code is found within this subdirectory:
  plugins/noarch/tcl/topotools1.7/topogromacs.tcl

Now, that being said, you should just run "package require topotools" to get
access to all of the associated commands.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>

On Mon, Jun 11, 2018 at 10:30:51PM +0200, Francesco Pietra wrote:
&amp;amp;gt; I would like to try porting to gromacs/charmm36 a protein-ligand system
&amp;amp;gt; built and running on namd/charmm36. To this end I was unable to find a
&amp;amp;gt; topotool folder, inclusive of topogromacs, on my installations of vmd
&amp;amp;gt; 1.9.4a12 or vmd 1.9.3. Although I know how to add third-part plugins to
&amp;amp;gt; vmd, I am confused here. Thanks for advice.
&amp;amp;gt;
&amp;amp;gt; francesco pietra 

--
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