[gmx-users] ProDrg

[Justin Lemkul]

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 
force fields.

-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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