Hi gontchar,<br><br>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.<br>
<br>Thanks,<br>Nitin<br><br><div class="gmail_quote">On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар <span dir="ltr"><<a href="mailto:gontchar@gmail.com">gontchar@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I think you have to use some special programm for this purpose.<br>
AutoDock, for example, will be the right choice.<br>
<br>
2012/4/12 sai nitin <<a href="mailto:sainitin7@gmail.com">sainitin7@gmail.com</a>>:<br>
<div><div class="h5">> Hi all,<br>
><br>
> I am working on protein - ligand molecular dynamics simulation using<br>
> gromacs. I have a protein in which i know binding site which is composed of<br>
> 5 residues and i have one ligand i have to place this in binding site.<br>
><br>
> Can any body tell me how to do place this ligand to binding site<br>
><br>
> Thanks in advance<br>
><br>
><br>
> Cheers<br>
> --<br>
><br>
> Sainitin D<br>
><br>
><br>
</div></div>> --<br>
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<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
--<br>
<br>
Андрей Гончар<br>
--<br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br><span><br>Sainitin D</span> <br><span>PhD student<br></span><span>Bioinformatics Group</span><br><span>
</span><span>Biotechnology Center</span><br><span>
Technische Universität Dresden<br>
Tatzberg 47/49<br>
01307 Dresden, Germany<br>Tel Lab:</span><span>+49 (0)351 463 40060</span><br>