[gmx-users] protein ligand simulation

[Justin Lemkul]

On 4/19/16 9:08 PM, bharat gupta wrote:
> 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
>>>> for Automatic Cleanup! (jalemkul at vt.edu) Add cleanup rule
>>>> <
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>>>>>
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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
>

Apparently you added your ligand to residuetypes.dat and called it Protein.  You 
have 3540 atoms that are identified as Protein by make_ndx; that encompasses the 
actual protein and the ligand.  You can still select the ligand by its residue 
name or number, but it won't appear in any selection lists as a separate entry 
if you tell GROMACS tools to consider it protein.  This will cause issues with 
some analysis tools like do_dssp and gmx chi.

-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

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