Hello Gmx user,
I would like to transport solute molecule from the ion channel (intracellular to extracellular site) using steered MD and umbrella sampling method to calculate the energy. I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but in distance.pl it shows some errors. I used the distance of pulling along the Z-axis but still it do not work. I found when I use distance as a pull-geometry, solute moves away from the channel rather transporting through channel. Then I tried direction as a pull-geoetry, then solute transported from the chanel,and generated pullf.xvg but not pullx.xvg file. I separated the trajectory using trjconv command gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o conf.gro -sep It generated conformations. Now I would like to calculate the COM distance between ion channel (protein) and solute (lig) using perl distance.pl but I received following error. Error readline() on closed filehandle IN at distances.pl line 16 Use of uminitialized value $distance in concatanation (.) or string at distances.pl line 30. Here is the distance.pl file which I used for this purpose which was downloaded from Dr. Lemkul's tutorial file. ----------------- #!/usr/bin/perl -w use strict; # loop g_dist command - measure distance in each frame, write to a file for (my $i=0; $i<=800; $i++) { print "Processing configuration $i...\n"; system("gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\' &>/dev/null"); } # write output to single file open(OUT, ">>summary_distances.dat"); for (my $j=0; $j<=800; $j++) { open(IN, "<dist${j}.xvg"); my @array = <IN>; my $distance; foreach $_ (@array) { if ($_ =~ /[#@]/) { # do nothing, it's a comment or formatting line } else { my @line = split(" ", $_); $distance = $line[1]; } } close(IN); print OUT "$j\t$distance\n"; } close(OUT); # clean up print "Cleaning up...\n"; for (my $k=0; $k<=800; $k++) { unlink "dist${k}.xvg"; } exit; ------------------------- this generated the summary_distances.dat with only frame numbers but there is no distance column in the file. Please help me to solve this issue Regards, Dr. Changdev G. Gadhe Post-Doc Researcher, Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850 Email: f07...@kist.re.kr -- 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.