Re: [gmx-users] Error while running perl distances.pl
Well to better understand what is going on I suggest:* use strict; line tells
to search for possible problems even if script can go on like it is.Maybe just
remove it?
* remove &>/dev/null or even better use other file instead of /dev/null like
dump.txt
You will see it that system call is all OK from print to screen or to that file.
* Edit all open functions into open or die style. Example:open(OUT,
">>summary_distances.dat") or die "can not open summary_distances.dat";If that
file open call fails you will see error like you wrote.* Examine all files
mentioned in script, they might be bad or not exist, that may hint to possible
issues.
On Wednesday, September 6, 2017, 10:42:30 AM GMT+3, 가디 장데부 고라크스나트
<f07...@kist.re.kr> wrote:
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: f07...@kist.re.kr
---Original message---
From: "Vytautas Rakeviius "<vytautas1...@yahoo.com>
To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장데부
고라크스나트<f07...@kist.re.kr>
Cc.: gadhe.chang...@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 $distance is the second row separated by space in
the file dist{number}.xvg which appears after execution of system callgmx
distance -s md_pull.tpr -f conf${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
<f07...@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 filefor (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 fileopen(OUT, ">>summary_distances.dat"); for (my $j=0; $j<=800; $j++) {
open(IN, "<dist${j}.xvg"); my @array = ; 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 upprint "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 t
Re: [gmx-users] Error while running perl distances.pl
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: f07...@kist.re.kr
---Original message---
From: "Vytautas Rakeviius "<vytautas1...@yahoo.com>
To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장데부
고라크스나트<f07...@kist.re.kr>
Cc.: gadhe.chang...@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
<f07...@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 = ;
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
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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
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, "
[gmx-users] Error while running perl distances.pl
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, "
[gmx-users] Error while running perl distances.pl
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, "
