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

[Joan Clark Nicolas]

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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