[gmx-users] pulling protein-ligand complex

abhisek Mondal abhisek.mndl at gmail.com
Sat Jan 7 23:21:03 CET 2017 

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?

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
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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
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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
>
> ==================================================
> --
> 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.
>



-- 
Abhisek Mondal

*Research Fellow*

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

*Kolkata 700032*

*INDIA*

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