[gmx-users] protein ligand simulation

[bharat gupta]

On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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:
>>
>> [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
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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.
>
Here's the link.
https://drive.google.com/open?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA


> -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
>
> ==================================================
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-- 
*Best Regards*
Bharat