Dear Adrian
I am sure about ligand because I used spdb viewer and computed H-bond
.ligand was correct place.
after amber running ligand replaced and exited . I used dist restraints for
fixing ligand but I cant!
if I put the restraints in active site,the vibrations will limit?!
I want to study the fast vibration in active site
Thanks from your answer
On Tue, Jul 12, 2011 at 4:18 AM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Dear Elahe.
>
> What proof do you have that the ligand is stable in the active site ?
>
> If it really moves too much, then maybe it should be there in the first
> place ?
>
> I do not know what type of restrains you put in there, but if they are
> distances, putting two or three different ones should not allow the
> ligand to move too much with respect to teh frame of reference of the
> active site.
>
>
>
> On 7/12/11 1:11 PM, e p wrote:
> > Dear Ambers
> > 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.
> > Thanks for your attention
> >
> > Elahe
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Adrian E. Roitberg
> Full Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
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>
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Received on Tue Jul 12 2011 - 23:00:03 PDT
