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 <[email protected]> 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 <[email protected]>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 <[email protected]>: >> > 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 [email protected] >> > 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 [email protected]. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- >> >> Андрей Гончар >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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