[gmx-users] pulling protein-ligand complex

Sat Jan 7 21:59:46 CET 2017

yes. 19 and 20.
I have been able to modify distances.pl and it is running well I guess. It
is taking a little time per configuration to process.

Is there any way to know if distances.pl program terminates normally and
calculations are successful ?

On Sun, Jan 8, 2017 at 2:20 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/7/17 3:36 PM, abhisek Mondal wrote:
>
>> 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.
>>
>
> What groups defined your reaction coordinate for the pulling?  Those are
> the groups you want.
>
> -Justin
>
>
> 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
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>>>>> 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
>>>
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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
>
> ==================================================
> --
> 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
>
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>

-- 
Abhisek Mondal

*Research Fellow*

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

*Kolkata 700032*

*INDIA*