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 <[email protected]>:
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
[email protected] | (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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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