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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Received on Tue Jul 12 2011 - 23:00:02 PDT
