[gmx-users] pulling protein-ligand complex

[Justin Lemkul]

On 1/7/17 2:51 PM, abhisek Mondal wrote:
> 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 ?
>

gmx distance failed.  Run gmx distance yourself and see what the error message 
is.  The script just executes gmx distance and assumes everything works because 
it's designed for a tutorial.  You may have to modify it to get it to work in 
your system; you can't assume it is plug-and-play.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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