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

[sai nitin]

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
>>> >
>>> >
>>> > --
>>> > 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!
>>> > Please don't post (un)subscribe requests to the list. Use the
>>> > www interface or send it to gmx-users-request at gromacs.org.
>>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>> --
>>>
>>> Андрей Гончар
>>> --
>>> 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!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>>
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 

Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120412/2308e0b8/attachment.html>