[gmx-users] ProDrg

[Hadházi Ádám]

I think, the R.E.D server (
http://q4md-forcefieldtools.org/REDServer-Development/) can be considered
as the "state of the art" for AMBER ff (at the moment), but it is not as
comfortable as ACPYPE, since its (the R.E.Ds) outputs are in AMBER format.

2014-12-10 16:40 GMT+10:00 Naba <nabajyoti.goswami at gmail.com>:

> How about ACPYPE for AMBER force field?
>
> On Tue, Dec 9, 2014 at 12:56 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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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>
>
> --
> Nabajyoti Goswami
>
> Research Associate
> Bioinformatics Infrastructure Facility
> Department of Animal Biotechnology
> College of Veterinary Science
> Khanapara,Guwahati 781022
> Assam, India
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