[gmx-users] problem with phosphorylated serine

Justin Lemkul jalemkul at vt.edu
Mon Nov 17 18:30:14 CET 2014

On 11/16/14 8:26 PM, Jayant James wrote:
> Hi !
> I downloaded the ffG43a1p.tar.gz
> <http://www.gromacs.org/@api/deki/files/12/=ffG43a1p.tar.gz> for
> simulations of phosphorylated serines (downloaded from
> http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
> running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
> error (below). Well there is no "HISE" in the input pdb file. There is a
> SEP. So I thought I'd better get help from the GMX community. I also found
> that if I were to execute a pdb file without any phosphorylated serine the
> pdb2gmx runs all the way to the end and the gives the error message similar
> to one below.

You downloaded the wrong files.  Note there is a specific version for 4.5 and 




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