Dear Carlos
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
Best
On Tue, Jul 12, 2011 at 4:20 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> How can you be sure that the initial docked position is fully correct? Do
> you know that the lugand is stably bound prior to the reaction? Are you
> sure
> the parameters for the ligand are good? There are many questions for which
> you are the only one that can best answer them.
> On Jul 12, 2011 7:12 AM, "e p" <epepgene1.gmail.com> 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
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Received on Tue Jul 12 2011 - 23:00:04 PDT
