[gmx-users] .rtp files

[Justin Lemkul]

On 6/19/14, 4:58 PM, Negar Parvizi wrote:
> Dear Gromacs users;
> I use Gromacs version 4.5.4. I finished protein-ligand complex tutorial(Dr.justin lemkul tutorial). Now i want to use my ligand. I am new in this field(charge group blocking). For getting an idea about charge group blocking, i check .rtp files.
>
> cheking aminoacides.rtp files of gromos force field , it has ATP charge group blocking, but i didn't understand it and also i didn't find many of molecules ex. : TEMP, BA, RTOL, ...
>
> It would be greatly appreciated if anyone can help me in this field?
>

You need to tell us what ligand you're dealing with.  A few other things to 
consider:

1. The manual has a very good description of what charge groups are and how 
they're designed.
2. If you're using PME, charge groups summing to zero or an integer is not 
strictly necessary.
3. If you're going to use the Verlet cutoff scheme for the simulation, charge 
groups are totally irrelevant.

-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

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