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

[rama david]

Hi Sai,
you have to concider the protein and ligand strucure  togather (Docked
structure ),

After these follow the link
(
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
)

With Best Wishes,
Rama

On Thu, Apr 12, 2012 at 5:13 PM, sai nitin <sainitin7 at gmail.com> wrote:

> 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
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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