I don't think AutoDock and Vina are suitable for peptide docking. I would first try the FlexPepDocking module of Rosetta which does ab initio folding of the peptide on the receptor, while moving the side-chains of the protein but leaves its backbone intact. Rosetta implements a knowledge-based scoring, which has been specifically designed for this task and is as fast as Vina or AutoDock.
I would first do that and if I wouldn't get any reasonable results then I would move to MD starting from the top scored protein-peptide complexes created by Rosetta. Thomas On 4 October 2012 15:08, rama david <ramadavidgr...@gmail.com> wrote: > Hi francesco, > > Thank you For reply. > I did docking but the result are not so impressive. > I used vina and autodock. > I also did virtual screening in autodock but the result are not upto the > mark. > > Is the freezing of group can affect my system?? How much efficiency I get > by these work?? > As these group are going to freeze in four simulation so if it affect one > ligand it affect other > ligand also. > > I read article that did the work like me , > they sliced the binding residues and used the inert solid sphere to > support binding residues > instead of the freezing group other group. > > I think both way should have same effect..Am I right or wrong?? > > If you have any other way please suggest it.. > > With best wishes and regards > Rama david > > > On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri > <francesco.ot...@gmail.com>wrote: > > > Hi, > > as far as I know, freezing just set velocities to 0 so you gain nothing > > freezing atoms. > > > > By the way, have you tried docking? It takes into account multiple > > conformation and > > orientation of the peptide and, depending upon the implemented algorithm, > > also > > protein sidechain orientation. > > > > Francesco > > > > > > 2012/10/4 rama david <ramadavidgr...@gmail.com> > > > > > thank you Justin for reply. > > > > > > I dont know about long range interactions. > > > But as I freeze the group I think it will improve my computational > speed. > > > So is there any way to find out or decide which group should be > > > freeze, and which group should affect my interaction most probably?? > > > > > > Should I do Essential Dynamics ??? or Principle component analysis ??? > > > > > > Would you suggest me any general protocol for such work?? > > > > > > Thank you in Advance > > > > > > > > > With Best Wishes and regards. > > > Rama David > > > > > > On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > > > > > On 10/4/12 2:01 AM, rama david wrote: > > > > > > > >> Hi gromacs Friends, > > > >> I want to do peptide-receptor ( Protein) interaction > > > >> study.Receptor consist a single chain. > > > >> Peptide is made up of 4 amino acids. I know the interaction > pattern > > of > > > >> peptide and receptor. > > > >> I plan to mutate single residue each at a time and run 4 > simulation . > > > >> So I will have the 4 different simulation that contain the mutated > > > >> residues > > > >> and the wild one. > > > >> > > > >> > > > >> Then afterward from the interaction energy I want to select the > > peptide > > > >> which is showing > > > >> stronger interaction than others. > > > >> > > > >> As mention I know the binding site, If I freeze the remaining > portion > > > in > > > >> receptor > > > >> that not involved in binding , Is it going to affect my screening > > > process > > > >> ??? > > > >> > > > >> > > > > Potentially. Do you know that the binding interactions and the > > mutations > > > > will only perturb local residues? Do you know that there are no > > > long-range > > > > motions to be considered? > > > > > > > > I think you gain very little by freezing portions of the system, and > > risk > > > > more than you gain. > > > > > > > > -Justin > > > > > > > > -- > > > > ==============================**========== > > > > > > > > Justin A. Lemkul, Ph.D. > > > > Research Scientist > > > > Department of Biochemistry > > > > Virginia Tech > > > > Blacksburg, VA > > > > jalemkul[at]vt.edu | (540) 231-9080 > > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > > > > > ==============================**========== > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > > > * Please search the archive at http://www.gromacs.org/** > > > > Support/Mailing_Lists/Search< > > > 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 gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > > > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > 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 gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > Cordiali saluti, Dr.Oteri Francesco > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > * Can't post? 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Read http://www.gromacs.org/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists