From: Francesco Pietra (
Date: Wed Jun 13 2018 - 08:42:25 CDT

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


On Wed, Jun 13, 2018 at 11:53 AM, Vermaas, Joshua <>

> 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
> list/vmd-l/28199.html).
> -Josh
> On 2018-06-11 15:36:21-06:00 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
> 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
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