[gmx-users] Interaction study for peptide-receptor..

[francesco oteri]

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 <ramadavidgroup at 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 <jalemkul at 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 at 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-request at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Cordiali saluti, Dr.Oteri Francesco