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 <[email protected]>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 <[email protected]> > > > 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 <[email protected]> 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 [email protected] > > > 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 [email protected]. > > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > > 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 > > > > > > -- > Cordiali saluti, Dr.Oteri Francesco > -- > 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? 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