Hi Sai,<br>you have to concider the protein and ligand strucure togather (Docked structure ),<br> <br>After these follow the link <br>(<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html</a>)<br>
<br>With Best Wishes,<br>Rama <br><br><div class="gmail_quote">On Thu, Apr 12, 2012 at 5:13 PM, sai nitin <span dir="ltr"><<a href="mailto:sainitin7@gmail.com">sainitin7@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
hi rama david,<br><br>Thank you for suggestion i looked up how to convert docked structure into PDB file it is described here<br><br><a href="http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock" target="_blank">http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock</a><br>
<br>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<br>OR<br>Should i consider complex PDB file (which consists of both protein + ligand)<br>
<br><br>Thanks in advance,<br>Sainitin<div class="HOEnZb"><div class="h5"><br><br><div class="gmail_quote">On Thu, Apr 12, 2012 at 10:57 AM, rama david <span dir="ltr"><<a href="mailto:ramadavidgroup@gmail.com" target="_blank">ramadavidgroup@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi sai,<br>you have to used docked structure to simulation .<br>1st convert the dock structure ,that you concider imptortant for <br>
your further study to pdb file (As you used autodock for docking ).<br>Then perform MD on that structure.<br>
<br>Have a nice day...<div><div><br><br><div class="gmail_quote">On Thu, Apr 12, 2012 at 2:14 PM, sai nitin <span dir="ltr"><<a href="mailto:sainitin7@gmail.com" target="_blank">sainitin7@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div><div><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" target="_blank">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" target="_blank">sainitin7@gmail.com</a>>:<br>
<div><div>> 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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<br>
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</font></span></blockquote></div><br><br clear="all"><br></div></div><span><font color="#888888">-- <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><a href="tel:%2B49%20%280%29351%20463%2040060" value="+4935146340060" target="_blank">+49 (0)351 463 40060</a></span><br>
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<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>
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