[gmx-users] ffbonded.itp

[Justin Lemkul]

On 5/24/16 6:20 AM, a.omidi at shirazu.ac.ir wrote:
> ​Hi
> I want to simulate a glycoprotein, I have defined a new residue with charmm36
> I should define some angles, bonds and dihedrals for this new residue in ffbonded.itp file,
> also in the ffbonded.itp file there is some other numbers and etc
> I dont know what are these and how to define correctly these parametres for my sugar in my protein

Start with Chapter 5 of the manual.

-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

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