[gmx-users] protein ligand simulation

bharat gupta bharat.85.monu at gmail.com
Wed Apr 20 03:22:26 CEST 2016


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

>
>
> 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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>>>>>
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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.

Okay, but it means that I have done something wrong while preparing the
files for the ligand. Actually, I didn't add the ligand to
residuetypes.dat, I did exactly what the protein-ligand tutorial mentioned.

Now, I got to know where the error is. I should rename my ligand instead of
using CT3. As, CT3 is already present in the residuetypes.dat file.
Atlast, after spending 2 horrible days at this, I can move forward with the
simulation.

Regarding the ligand parameters after optimization (from ATB server), I
already checked the post you mentioned earlier. But, my doubt is whether is
it reasonable to use the unoptimized ligand for simulation ??

Also, I am using gromacs v 5.0.4 and I want to use the tool g_puckering
which was written for v 4.x.x. I am not able to compile that, so could you
recommend so other tool to calculate cremer pople parameters for sugar
puckering, as my ligand is a trisaccharide ?

Thanks Justin


>
> -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


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