[gmx-users] charge groups

[Justin Lemkul]

On 6/10/14, 12:58 AM, Negar Parvizi wrote:
> Dear Dr.Lemkul,
>
>
>
>
>
> Thank you very much for your reply. It was very helpful to me.
> I checked the force field .rtp files. Here I have two questions:
> 1-Checking the .rtp files of gromos force field, I saw that always  one hydrogen of NH2 and also the OH group of COOH were not included in the
> charge groups.
> On the other hand, in your paper ( Practice Consideration for building
> GROMOS-Compatiple Small-Molecule Topologies) I noticed that you have
> replaced these NH2 and COOH groups with NHCH3 and COCH3. I did not
> understand this. Would you please explain why you did that ?
>
> Should we do the same modifications  for all NH2 and COOH groups, either when
> these groups belong to an aminoacid or any other molecule?
>
> 2- Is there any straightforward strategy for specifying charge groups of
> a ligand? If so, could you please introduce me a reference for that?
>
> As always, your response would be greatly appreciated.

I answered this yesterday:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-June/089821.html

-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

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