[gmx-users] pulling protein-ligand complex

Justin Lemkul jalemkul at vt.edu
Mon Jan 9 14:02:47 CET 2017 


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-L5Y7BiGJT29hSGlEWTM3Zk0?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
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>>>>>>>>>>>> -users
>>>>>>>>>>>> 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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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> 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
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>> /Mailing_Lists/GMX-Users_List before posting!
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>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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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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>>>> * Please search the archive at http://www.gromacs.org/Support
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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
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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

==================================================

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