[gmx-users] Error while running perl distances.pl

["가디 장데부 고라크스나트"]

Hello Vytautas,


I changed the script file to


gmx_mpi_d 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\"\'





rest is same


but it showed the same error as previous one.


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.





Could you help me out to solve this issue.



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: F07338 at kist.re.kr










 


-----------------------Original message-----------------------
From: "Vytautas Rakeviius "<vytautas1987 at yahoo.com>
To: gmx-users at gromacs.org,gromacs.org_gmx-users at maillist.sys.kth.se,가디 장데부 고라크스나트<f07338 at kist.re.kr>
Cc.: gadhe.changdev at gmail.com
Sent date: 2017-09-04 15:36:29 GMT +0900 (Asia/Seoul)
Title: Re: [gmx-users] Error while running perl distances.pl








Script assumes that variable $distance is the second row separated by space in the file dist{number}.xvg which appears after execution of system call

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\"\'


I just think that dist{number}.xvg creation fails for you in first place because "gmx distance" in the script is not adjusted according to your system.

You use _mpi_d in your post.












On Monday, September 4, 2017, 5:48:43 AM GMT+3, 가디 장데부 고라크스나트 <f07338 at kist.re.kr> wrote:











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: F07338 at 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-request at gromacs.org.