[gmx-users] pulling protein-ligand complex

[abhisek Mondal]

So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2.

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

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
>
> ==================================================
> --
> 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.
>



-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*