jalemkul at vt.edu
Mon Dec 8 20:26:19 CET 2014
On 12/8/14 2:12 PM, xy21hb wrote:
> Dear all,
> Since Justin mentioned in previous mails that PRODRG is almost unreliable,
> is there any reliable source for patching a new small molecule for gromacs, in general?
When it comes to force fields, you can't speak in generalities. Any new species
must be parametrized in accordance with the methods of the parent force field,
for balance and consistency. The ATB server is significantly better than PRODRG
for Gromos-compatible compounds. There are other servers for other force fields
(ParamChem for CHARMM/CGenFF, etc) but no black-box method should be trusted
without scrutinizing and testing extensively.
The bottom line is that parametrization of new species is hard, and it often
requires significant effort in finding suitable target data, refining parameters
to match, then validating that those parameters are actually useful in
subsequent simulations. This is common across all simulation codes and all
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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