VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jun 13 2018 - 04:53:57 CDT

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).

-Josh

On 2018-06-11 15:36:21-06:00 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

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 

--
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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