Hi Sai, you have to concider the protein and ligand strucure togather (Docked structure ),
After these follow the link ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html ) With Best Wishes, Rama On Thu, Apr 12, 2012 at 5:13 PM, sai nitin <[email protected]> wrote: > 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 > > -- > 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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