[gmx-users] pdb file for united atom force fields

[Justin Lemkul]

On 8/12/15 12:46 AM, faride badalkhani wrote:
> Dear Gromacs users,
>
> I need to work with a united atom FF, but I have defined all the Hydrogens
> in my pdb file. Does it cause any problem in MD procedure?
>

Well, the UA force field won't use (most of) the H, so they obviously need to be 
removed.  If this is a biomolecule, pdb2gmx -ignh takes care of this for you.

-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

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