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 ? -- 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.
