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

[Андрей Гончар]

According to this
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html)
tutorial, you have to combine your target protein and your ligand.
First of all, use pdb2gmx to generate gromacs topologies and coordinates.
After that merge protein.gro with ligand.gro. Don't forget to correct
your protein.top including there ligand.top.
You can find the full process of protein/ligand simulation in the tutorial.

2012/4/12 sai nitin <sainitin7 at gmail.com>:
> 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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-- 

Андрей Гончар