[gmx-users] RMSF problem

Justin Lemkul jalemkul at vt.edu
Fri May 12 13:51:28 CEST 2017

On 5/11/17 1:43 PM, Franco Henrique wrote:
> Dear Justin Lemkul,
> Thank’s for prompt reply.
> My protein has 198 aminoacides (PDB: 2GOJ; http://www.rcsb.org/pdb/explore.do?structureId=2GOJ). After RMSF command (gmx rmsf -f .xtc -s .tpr -o .xvg -res), the output has only 103 aminoacides as visualized by Grace software. I am running gromacs 5.1.2 in ubuntu.
> Any inquiries are more than welcome.

Your full screen output and an upload of the output file (to a file-sharing 
service, as the list does not accept attachments) would be helpful.  There's no 
logical reason for gmx rmsf to randomly ignore residues.  Did you 
simulate/analyze the whole dimer structure, or just one chain?



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