[gmx-users] pulling protein-ligand complex

[abhisek Mondal]

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*