From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jun 13 2018 - 09:35:04 CDT

I forgot saying that the velocities are not necessary for FEP, at least so
with NAMD, where the velocitie are generated ex novo at each lambda.

francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Jun 13, 2018 at 4:30 PM
Subject: Re: vmd-l: topotools/topogromacs
To: "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>, "johns_at_ks.uiuc.edu" <
johns_at_ks.uiuc.edu>

Hi Josh: referring to the way FEPs can be run with NAMD, it is sufficient
to have a system running MD, to which flags for FEP can be added. I hope
the same applies to GROMACS. If so, no need to extend TOPOGROMACS. I have
first to become familiar with GROMACS, where plenty of studies of
protein-ligand FEP have appeared in the literature.

Thanks again
francesco

On Wed, Jun 13, 2018 at 4:10 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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
> > 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_l
>> ist/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 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 <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaps.google.com%2F%3Fq%3Dof%2BIllinois%2C%2B405%2BN.%2BMathews%2BAve%2C%2BUrbana%2C%2BIL%2B61801%26entry%3Dgmail%26source%3Dg&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cf487d9a59cc24043c77008d5d13380a1%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636644941505513315&sdata=WVonXnXihL3vjvnEbOzwmn7kcaxqtiiaDviyDKOk0Mc%3D&reserved=0>https://na01.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~johns%2F&amp;amp;amp;data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C77fe722908db4cc2bdc108d5cfe35eb2%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636643497810593595&amp;amp;amp;sdata=Si4CHOUJ%2FGEedPBReaZmLFohgkTSuXYLE8c%2Bd5FL1%2BQ%3D&amp;amp;amp;reserved=0 Phone: 217-244-3349https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2F&amp;amp;amp;data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C77fe722908db4cc2bdc108d5cfe35eb2%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636643497810593595&amp;amp;amp;sdata=eFyk21SZAIlk%2Ba%2FS38My78ul2f8LyZeYZYDzoaMqrNY%3D&amp;amp;amp;reserved=0
>>
>>