[gmx-users] Problem with GROMACS and AMBER ff

[Justin Lemkul]

On 6/15/15 4:49 PM, Celia wrote:
>
> Hi all. We doing a MD simulation with GROMACS using AMBER force field.
> During the simulation the disulfide bonds are increasing over time. We set
> the bridge manually with pdb2gmx. Someone help us?
>

Probably something went wrong with this manual hack.  If pdb2gmx didn't assign 
it, then the geometry probably wasn't amenable to creating a disulfide, in which 
case you have to do some refinement first.  If you manually added a bond, did 
you correctly assign the right side chain state for CYS (i.e. not the thiol 
form) and add all other angles and dihedrals correctly?

-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

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