So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2.
The catch here to analyze the COM distances between 2 pull groups. Am I getting that right ? On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 2:51 PM, abhisek Mondal wrote: > >> Hi, >> I'm pulling ligand out of protein using umbrella sampling method in >> gromacs-4.6.2. >> Using "trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep" command generated >> 500 different files (selected "SYSTEM" in interactive prompt, need to >> study >> protein and ligand simultaneously). But when I use "perl distances.pl" >> command I get none of the distances calculated. >> Following output was generated: >> >> ... >> Processing configuration 497... >> Processing configuration 498... >> Processing configuration 499... >> Processing configuration 500... >> readline() on closed filehandle IN at distances.pl line 16. >> Use of uninitialized value $distance in concatenation (.) or string at >> distances.pl line 30. >> readline() on closed filehandle IN at distances.pl line 16. >> Use of uninitialized value $distance in concatenation (.) or string at >> distances.pl line 30. >> readline() on closed filehandle IN at distances.pl line 16. >> Use of uninitialized value $distance in concatenation (.) or string at >> distances.pl line 30. >> readline() on closed filehandle IN at distances.pl line 16. >> Use of uninitialized value $distance in concatenation (.) or string at >> distances.pl line 30. >> readline() on closed filehandle IN at distances.pl line 16. >> ... >> >> >> Help me out here. What did go wrong ? >> >> > gmx distance failed. Run gmx distance yourself and see what the error > message is. The script just executes gmx distance and assumes everything > works because it's designed for a tutorial. You may have to modify it to > get it to work in your system; you can't assume it is plug-and-play. > > -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. > -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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.
