[gmx-users] Virtual Sites in protein-ligand systems

[Alan]

No, ACPYPE won’t give VS. But if I learn more about, I can try to
implement. No guarantee though.

On 30 October 2015 at 10:11, Joan Clark Nicolas <joan.clark88 at gmail.com>
wrote:

> I am trying to run MD calculations using a 5 fs timestep, so I need tu use
> Virtual Sites. The problem is that I generate ligand topology with acpype
> and then I add it to the protein topology, so the VS of the ligand are not
> generated. Maybe there is a way to generate VS for the ligand with acpype?
>
> And, about the [ virtual_sites* ] directive, can you tell me where can I
> read about this? maybe this is the thing I am looking for.
>
> Thank You!
>
>
>
> *Joan Clark i Nicolas*
>
> 2015-10-29 18:18 GMT+00:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:
> >
> >> Dear gmx users,
> >> I am trying to run MD calculations on a protein-ligand system using
> >> Virtual
> >> Sites, but as I generate my protein and ligand topologies separately
> (with
> >> pdb2gmx and acpype, respectively), the VS for the ligand are not
> >> generated.
> >>
> >> Does anyone know a way to generate the VS for the ligand without adding
> it
> >> to the force field?
> >>
> >>
> > One can define any [ virtual_sites* ] directive manually in the topology.
> > pdb2gmx can build some types of virtual sites, but you'd have to tell us
> > specifically what it is you're trying to do if you want anything really
> > useful.  Soon I will upload a patch that will make virtual site
> > construction easier, and intrinsic to pdb2gmx.  I just need to find the
> > time to work out the kinks...
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588