[gmx-users] GROMOS atp file
farideh.khamseh at gmail.com
Sat Aug 15 15:51:53 CEST 2015
But all the nonbonded parameters for these Hydrogens are zero while they
are polar and they should be considered
On Sat, Aug 15, 2015 at 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
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> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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