[gmx-users] CHARMM-GUI files give error in Gromacs

Justin Lemkul jalemkul at vt.edu
Fri Sep 2 16:40:53 CEST 2016

On 9/2/16 10:39 AM, gozde ergin wrote:
> Hi Justin,
> I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction.
> What should I change in CHARMM-GUI files?

Nothing.  That's my point.  When the system is constructed, CHARMM-GUI builds a 
PSF and list of force field parameters that it needs.  This information is then 
converted to GROMACS format.  CHARMM-GUI does an energy evaluation to confirm 
that everything is present.  That's why it's a bit mystifying that GROMACS 
fails; by definition, the system, topology, and force field have already been 
checked for integrity.



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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