[gmx-users] pulling protein-ligand complex
abhisek Mondal
abhisek.mndl at gmail.com
Sun Jan 8 18:34:24 CET 2017
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".
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!
>>>>>>>>>>>
>>>>>>>>>>> * 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
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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!
>>>>>>>
>>>>>>> * 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!
>>>>>
>>>>> * 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
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>>
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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
> /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*
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