[gmx-users] PRODRG -cgnr

[Justin Lemkul]

On 7/28/14, 2:05 AM, Atila Petrosian wrote:
> Dear Justin
>
> Thanks for your answer.
>
> I want to use GROMOS96 43a1 force field for my protein and PRODRG
> parameters for my ligand.
>
> I want to use leap-frog algorithm for integrator. Based on your opinion, I
> don't use QM charges.
>
> In these conditions, I will use my first way mentioned in my previous email.
>
> Is my manner true?
>

If your molecule is comprised totally of existing functional groups, there's 
generally no need to reparametrize anything unless you discover a specific 
deficiency.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================