[gmx-users] GROMOS atp file

Justin Lemkul jalemkul at vt.edu
Sat Aug 15 13:47:48 CEST 2015

On 8/15/15 4:42 AM, faride badalkhani wrote:
> Dear all,
> I am having a question about Hydrogens in GROMOS FF. There are two
> Hysrogens in .atp file of GROMOS FF as follows:
>     HC   1.00800 ;     hydrogen bound to carbon
>        H   1.00800 ;     hydrogen not bound to carbon
> and all the nonbonded parameters for H are considered zero, but what about
> polar Hydrogens that are bounded to elements other than C (for example H in
> amino or amid groups)? How should I treat with these polar hydrogens?

That's what atom type H is - "hydrogen *not* bound to carbon."



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


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