[gmx-users] RMSF problem
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
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