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

Justin Lemkul jalemkul at vt.edu
Thu Oct 29 19:18:26 CET 2015

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 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


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