[gmx-users] protein ligand simulation

[bharat gupta]

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 ??

>
> 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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-- 
*Best Regards*
Bharat