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.
