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

[rama david]

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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