[gmx-users] hydrogen atom parameter definition for charmm 36

Justin Lemkul jalemkul at vt.edu
Sat Apr 9 17:56:01 CEST 2016

On 4/9/16 11:44 AM, Nikhil Maroli wrote:
> Hi,
> i am following this method
> (http://www.sciencedirect.com/science/article/pii/S0010465514002240)
> so when i run the script it has to  generate gro file for all the 1000
> pdb's (100ns MD) , inserting *.itp and *.prm files will take lots of time
> for each steps ;) ,i dont have knowledge in perl or python to make a
> script for this .
> could you please suggest me any method for this ?!

The topology for any classical MD simulation is constant; there is no need to 
regenerate anything.  You have a topology from when you ran the MD, so why do 
you need to regenerate it now?  I have not used this MM/PBSA program, but if 
there are specific issues with it you should contact its developers and ask for 
their suggestions.  This isn't really a GROMACS issue, per se.



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


More information about the gromacs.org_gmx-users mailing list