[gmx-users] RMSF problem

Franco Henrique fhpharm at gmail.com
Thu May 11 19:44:02 CEST 2017

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.

Best regards,
Franco Henrique.
Doutor em Biotecnologia
Professor Assistente B 
Departamento de Saúde - DSAU
Universidade Estadual de Feira de Santana - UEFS
Avenida Transnordestina s/n, bairro Novo Horizonte CEP 44.036-900 - Feira de Santana – BA

Em 11 de mai de 2017, à(s) 14:28, Justin Lemkul <jalemkul at vt.edu> escreveu:

On 5/11/17 1:21 PM, Franco Henrique wrote:
> Dear,
> I am have problem with RMSF data, because after I apply this command-line: gmx rmsf -f xxx.xtc -s yyy.tpr -o zzz.xvg -res, the .xvg file has not all residues of protein. If possible, I would like to know a tip to solve this problem.

How many residues do you have, and how many did the program output?  No GROMACS program will magically get rid of anything; it will analyze what you tell it to, so without more information about what you did, which group you chose, etc. it's hard to suggest anything.



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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