[gmx-users] pulling protein-ligand complex

abhisek Mondal abhisek.mndl at gmail.com
Mon Jan 9 15:20:11 CET 2017 

Alright. But can you please tell me what is the strategy of defining a
pull-vec ? The standard tutorial does not tell anything about it, if I got
it right.

Can you provide me some basics regarding pull-vec ?


On Mon, Jan 9, 2017 at 6:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/8/17 12:34 PM, abhisek Mondal wrote:
>
>> Sincere apologies...
>> I have uploaded the files here...
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJT29hSGlE
>> WTM3Zk0?usp=sharing
>>
>> I'm running another pull experiment with "pull_rate1 =0.01".
>>
>>
> You probably need to define a more suitable vector for pulling.  Your
> current approach appears to accomplish nothing, and a faster pull rate will
> not change that.
>
>
> -Justin
>
>
>> On Sun, Jan 8, 2017 at 10:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/8/17 1:52 AM, abhisek Mondal wrote:
>>>
>>> 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.
>>>>
>>>>
>>>> The list does not accept attachments (if I had a nickel for every time I
>>> said this...) so upload the files somewhere and provide a link.
>>>
>>>
>>> -Justin
>>>
>>>
>>> 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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>>>>>>>>>>>>>
>>>>>>>>>>>>> * For (un)subscribe requests visit
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>>>>>>>>>>>>> -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!
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>>>>>>>>>>> -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
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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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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>> ==================================================
>>>>>
>>>>> 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
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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
>
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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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