[gmx-users] pulling protein-ligand complex

abhisek Mondal abhisek.mndl at gmail.com
Sat Jan 7 21:36:06 CET 2017


Alright, I'm trying.
Please tell me one thing, given the fact I want to analyse the
protein-ligand pull scenario, what should be my choice during the prompt i
get after executing "g_dist_mpi -s pull.tpr -f conf200.gro -n index.ndx -o
all"

Reading file pull.tpr, VERSION 4.6.2 (single precision)
Group     0 (         System) has 2648311 elements
Group     1 (        Protein) has  1693 elements
Group     2 (      Protein-H) has  1301 elements
Group     3 (        C-alpha) has   163 elements
Group     4 (       Backbone) has   489 elements
Group     5 (      MainChain) has   653 elements
Group     6 (   MainChain+Cb) has   805 elements
Group     7 (    MainChain+H) has   815 elements
Group     8 (      SideChain) has   878 elements
Group     9 (    SideChain-H) has   648 elements
Group    10 (    Prot-Masses) has  1693 elements
Group    11 (    non-Protein) has 2646618 elements
Group    12 (          Other) has    15 elements
Group    13 (            JZ4) has    15 elements
Group    14 (             NA) has  1602 elements
Group    15 (             CL) has  1608 elements
Group    16 (          Water) has 2643393 elements
Group    17 (            SOL) has 2643393 elements
Group    18 (      non-Water) has  4918 elements
Group    19 (Protein_chain_A) has  3210 elements
Group    20 (            JZ4) has    15 elements
Group    21 (             NA) has  1602 elements
Group    22 (             CL) has  1608 elements
Group    23 ( Water_and_ions) has 2646603 elements
Group    24 (        r_1-163) has  5605 elements
Group    25 (          r_164) has    39 elements

Do I go with System ? I only need to see protein-ligand pull though.
Can you give me some suggestions ?

On Sun, Jan 8, 2017 at 1:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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


More information about the gromacs.org_gmx-users mailing list