[gmx-users] How to fit ligand in specific site in protein in simulation

sai nitin sainitin7 at gmail.com
Thu Apr 12 13:43:27 CEST 2012


hi rama david,

Thank you for suggestion i looked up how to convert docked structure into
PDB file it is described here

http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock

But i have one doudt about which structure to take should i consider
docking results produced by autodock DLG file (docking log file) which
consists of different docked conformations
OR
Should i consider complex PDB file (which consists of both protein + ligand)


Thanks in advance,
Sainitin

On Thu, Apr 12, 2012 at 10:57 AM, rama david <ramadavidgroup at gmail.com>wrote:

> Hi sai,
> you have to used  docked structure to simulation .
> 1st convert the dock structure ,that you concider imptortant for
> your further study to  pdb file (As you used autodock for docking ).
> Then perform MD on that structure.
>
> Have a nice day...
>
>
> On Thu, Apr 12, 2012 at 2:14 PM, sai nitin <sainitin7 at gmail.com> wrote:
>
>> Hi gontchar,
>>
>> I have done docking analysis using autodock using that ligand and binding
>> site but i want to do molecular dynamics (MD) using gromacs of same ligand
>> and binding site of my protein. Thats why i want to know how to place
>> ligand in specific binding site and run MD using gromacs.
>>
>> Thanks,
>> Nitin
>>
>>
>> On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар <gontchar at gmail.com>wrote:
>>
>>> I think you have to use some special programm for this purpose.
>>> AutoDock, for example, will be the right choice.
>>>
>>> 2012/4/12 sai nitin <sainitin7 at gmail.com>:
>>> > Hi all,
>>> >
>>> > I am working on protein - ligand molecular dynamics simulation using
>>> > gromacs. I have a protein in which i know binding site which is
>>> composed of
>>> > 5 residues and i have one ligand i have to place this in binding site.
>>> >
>>> > Can any body tell me how to do place this ligand to binding site
>>> >
>>> > Thanks in advance
>>> >
>>> >
>>> > Cheers
>>> > --
>>> >
>>> > Sainitin D
>>> >
>>> >
>>> > --
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>>>
>>> --
>>>
>>> Андрей Гончар
>>> --
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>>
>>
>>
>> --
>>
>> Sainitin D
>> PhD student
>> Bioinformatics Group
>> Biotechnology Center
>> Technische Universität Dresden
>> Tatzberg 47/49
>> 01307 Dresden, Germany
>> Tel Lab:+49 (0)351 463 40060
>>
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>
>
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-- 

Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
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