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
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