[gmx-users] pulling protein-ligand complex

abhisek Mondal abhisek.mndl at gmail.com
Sun Jan 8 07:52:20 CET 2017 

Alright. I'm attaching md_pull.mdp and sumary_distances.dat file.

May be I have set pulling rate very low. Anyway have a look.


On Sun, Jan 8, 2017 at 6:03 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/7/17 5:20 PM, abhisek Mondal wrote:
>
>> It finished normally then. I got another question. I was pulling along XZ
>> plane. Distances I got is not a arithmetic progression with respect to
>> different configurations. I mean the output looks like:
>> 50 1.3637913
>> 51 1.3729873
>> 52 1.4363521
>> 53 1.4652436
>> 54 1.4503893
>> 55 1.4260585
>> 56 1.3836564
>> 57 1.3918289
>> 58 1.3942112
>> 59 1.4296075
>> 60 1.4574580
>> 61 1.3772060
>> 62 1.3604678
>> 63 1.3986934
>> 64 1.3650020
>> 65 1.3965892
>> 66 1.4247549
>> 67 1.4097543
>> 68 1.4460622
>> 69 1.3933917
>> 70 1.4080330
>> 71 1.4576371
>> 72 1.4678355
>> 73 1.4853811
>> 74 1.4144009
>> 75 1.4365107
>> 76 1.4342467
>> 77 1.4353391
>> 78 1.4025292
>> 79 1.4092745
>> 80 1.4392823
>> 81 1.4330521
>> 82 1.4404603
>> 83 1.3839875
>> 84 1.3936158
>> 85 1.3747249
>> 86 1.4166344
>> 87 1.3945516
>> 88 1.3606738
>> 89 1.3709180
>> 90 1.3676665
>> 91 1.3724216
>> 92 1.3779051
>> 93 1.3530073
>> 94 1.3227006
>> 95 1.3054955
>> 96 1.2701077
>> 97 1.3492427
>> 98 1.3388848
>> 99 1.3286418
>> 100     1.3590064
>> 101     1.3886772
>> 102     1.3654326
>> 103     1.3153005
>> 104     1.3110788
>> 105     1.2885991
>> 106     1.3051655
>> 107     1.3151547
>> 108     1.3163824
>> 109     1.3328680
>> 110     1.3280408
>>
>> In such a case how am I to decide which ones to take as a starting
>> configurations ? Can you please give me an idea?
>>
>>
> It would help to have a full explanation of what you're doing, including
> .mdp files.  Getting partial details along the way makes it hard to give
> any useful advice.
>
> It looks like your species just oscillated over a range of 0.1 nm, which
> achieves very little, if anything, and certainly nothing resembling
> dissociation between the two.
>
>
> -Justin
>
> On Sun, Jan 8, 2017 at 2:34 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/7/17 3:59 PM, abhisek Mondal wrote:
>>>
>>> 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 ?
>>>>
>>>>
>>>> You won't get error messages and you will get a data file with distances
>>> vs. configuration number.
>>>
>>>
>>> -Justin
>>>
>>> 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
>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>
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>>>>>>>>>
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>>>>>>>>> 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!
>>>>>>>
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>>>>>>> or
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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!
>>>>>
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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
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>>
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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
>
> * For (un)subscribe requests visit
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> 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*

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