restraints in active site? in residues that interaction with ligand?
Do not the vibrations limit?
are you sure?
Thanks a lot
On Tue, Jul 12, 2011 at 11:45 PM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> Just run preliminary equilibration stage with restraint prior to MD
> without restraints.
>
> On Wed, Jul 13, 2011 at 9:35 AM, e p <epepgene1.gmail.com> wrote:
> > Dear Dmitry
> > I dont want to limit the vibrations because I want to study about
> vibrations
> > in active site .
> > Do you know that the restraints in active site limit the vibration or
> not?
> > thanks for your answer
> > Best
> >
> >
> > On Tue, Jul 12, 2011 at 4:30 AM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> >
> >> I would restrain the distance between ligand atoms involved in
> >> catalysis and active site residues at the equilibration stage. What is
> >> the reason to apply restraint on atoms that are not involved in
> >> catalysis?
> >>
> >> > I want to inspect the effect of connection of a ligand to my protein
> >> before
> >> > formation of a covalent bond to the active site. I have designed a
> new
> >> > ligand and put it to the active site by auto dock. the ligand moved
> >> during
> >> > MD run so I had to put dist restraints(rk2=50,) on ligand atoms that
> are
> >> not
> >> > involved in catalysis and on 5 residues of the protein out of the
> active
> >> > site. it didnt solve the problem. the ligand still moves and
> rotates.As I
> >> > want to study the vibrations before formation of nucleophilic attack,
> I
> >> dont
> >> > want to use restraints to limit active site vibrations.
> >> > Any offer would be apprecited.
> >> >
> >> >
> >> > Elahe
> >> > _______________________________________________
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> >> >
> >>
> >>
> >>
> >> --
> >> Dmitry Nilov
> >> Faculty of Bioengineering and Bioinformatics,
> >> Lomonosov Moscow State University
> >> web: http://enzyme.fbb.msu.ru/
> >>
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> >>
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> >
>
>
>
> --
> Dmitry Nilov
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
> web: http://enzyme.fbb.msu.ru/
>
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Received on Wed Jul 13 2011 - 02:30:02 PDT
