[gmx-users] (no subject)

[Justin Lemkul]

On 6/16/17 8:03 AM, Shivangi Agarwal wrote:
> Hi all
> 
> When i am generating a ligand topology using PRODRG, I am getting topology
> file with hydrogens deleted in it. Which another server can I use for
> ligand topology generation?
> 

GROMOS is a united-atom force field, so the aliphatic H atoms are not going to 
be explicitly represented; you should check your assumptions about force fields 
and which one you should be using if this comes as a surprise :)  PRODRG is not 
of sufficient quality for MD simulations without significant manual revision. 
ATB is better if you want to use a GROMOS parameter set.

-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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