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

[Justin Lemkul]

On 10/30/15 6:11 AM, Joan Clark Nicolas 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?
>

At present, the simplest way forward is to take the information you have in your 
ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to 
process the whole thing and build the virtual sites on the ligand.

> 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.
>

You can do this, but in addition to specifying the virtual sites (read in the 
PDF manual, it's all there), you will need to make the appropriate conversions 
in the [atoms] section and also build the coordinates for all virtual sites 
(e.g. the things that pdb2gmx does).

-Justin

> 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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-- 
==================================================

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

==================================================