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 <[email protected]>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 <[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 >> > > > -- > 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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