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 <jalem...@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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
