[gmx-users] PTM force field

Justin Lemkul jalemkul at vt.edu
Thu Dec 18 11:54:25 CET 2014

On 12/17/14 4:39 PM, Jianqing Xu wrote:
> Dear GMX Users,
> I am trying to simulate a protein with a cysteine sulfenic acid (Cys-SOH).
> I notice that both AMBER and GROMOS force field should have the parameters
> for residues having post-translational modifications :
> http://selene.princeton.edu/FFPTM/
> http://vienna-ptm.univie.ac.at/
> PTM-GROMOS can be downloaded and used in GROMACS without problems. However,
> looks like the PTM-AMBER force field can only be used in AMBER package, it
> it correct?  For some historical reasons, I am looking for the possibility
> to consistently use AMBER force field. I was wondering whether PTM-AMBER is
> ready yet for GROMACS?

If the parameters exist, the only challenge is unit conversion and writing them 
in Gromacs format.  Gromacs has supported Amber force fields for a decade.



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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