[gmx-users] Using a forcefield from NAMD

[Justin Lemkul]

On 4/21/14, 3:02 PM, Ali Khan wrote:
> Hi,
>
> I am interested in incorporating a nitroxide spin label into my protein
> simulation. I want to use the Charmm36 force field, and to my knowledge
> there is no force field for the MTSL spin label in charmm36 for gromacs.
> What I do have is a charmm22 force field of the MSTL label from NAMD. Is
> there a way to incorporate this NAMD force field into my gromacs
> simulations.
>

You've got parameters in one format, and you need them in another, so all you 
need to do is convert them.  If you've got a stream file that you're reading 
into NAMD, our Python script should do the job for you.  Look for 
cgenff_charmm2gmx.py:

http://mackerell.umaryland.edu/CHARMM_ff_params.html

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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