[gmx-users] protein ligand simulation

[Justin Lemkul]

On 4/19/16 9:01 PM, bharat gupta wrote:
> Thanks for your prompt response.
>
> On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
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>> On 4/19/16 8:28 PM, bharat gupta wrote:
>>
>>> Hi Justin,
>>>
>>> Here's the link for following files: complex.gro, CT3.itp (ligand
>>> topology), CT3.gro (ligand coordinates) and topology.top.
>>>
>>> https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA&usp=drive_web
>>>
>>> When I run make_ndx command using the solvated complex file (solv.gro), I
>>> don't find the ligand in any of the groups. Here's the output of that
>>> command:
>>>
>>> Command line:
>>>     make_ndx -f solv.gro -o index.ndx
>>>
>>>
>>> Reading structure file
>>> Going to read 0 old index file(s)
>>> Analysing residue names:
>>> There are:   368    Protein residues
>>> There are: 14227      Water residues
>>> Analysing Protein...
>>>
>>>     0 System              : 46221 atoms
>>>     1 Protein             :  3540 atoms
>>>     2 Protein-H           :  2746 atoms
>>>     3 C-alpha             :   367 atoms
>>>     4 Backbone            :  1101 atoms
>>>     5 MainChain           :  1470 atoms
>>>     6 MainChain+Cb        :  1795 atoms
>>>     7 MainChain+H         :  1826 atoms
>>>     8 SideChain           :  1714 atoms
>>>     9 SideChain-H         :  1276 atoms
>>>    10 Prot-Masses         :  3540 atoms
>>>    11 non-Protein         : 42681 atoms
>>>    12 Water               : 42681 atoms
>>>    13 SOL                 : 42681 atoms
>>>    14 non-Water           :  3540 atoms
>>>
>>>
>> Then solv.gro clearly doesn't contain your ligand; you haven't constructed
>> the system properly.
>>
> I have did exactly what the tutorial mentioned about ligand topology
> preparation. I have sent you the files as well (complex.gro, topol.top).  I
> did this preparation at least 2-3 times but every time  I don't get the
> ligand. Did you have a look at these files ??
>

Your problem is with solv.gro, and since none of the files provided are 
solv.gro, they are not relevant.

-Justin

>>
>> Also, when I ran pdb2gmx command for my protein, I got two files :
>>> porse_Protein_chainA.itp and chainA2.itp. Does that mean somewhere the
>>> protein chain is broken in the initial structure?
>>>
>>>
>> This just means you have multiple chains.
>>
>> For, my ligand I generated the parameters using ATB server, but the problem
>>> is that when I used the optimized geometry and itp files for the ligand,
>>> it's located far away from the active site. So, should I used the
>>> unoptimized geometry coordinates in that case, but wouldn't it be wrong to
>>> use the unoptimized geometry??
>>>
>>>
>> Do not optimize the geometry; you need the ligand's bound state to avoid
>> such problems.  This issue came up in another thread just a few hours ago
>> (it pays to read others' posts - quite often you'll learn something :)
>>
>> -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
>>
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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

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