[gmx-users] pulling protein-ligand complex

[Justin Lemkul]

On 1/7/17 3:24 PM, abhisek Mondal wrote:
> So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2.
>

If you're using an old version, the syntax is totally different, so you will 
have to make lots of changes to the script (or not use it at all).

> The catch here to analyze the COM distances between 2 pull groups. Am I
> getting that right ?
>

Yes.

-Justin

> On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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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>
>
>

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

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

==================================================