[gmx-users] ProDrg

[Naba]

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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India