Re: [AMBER] dist restraint

From: e p <>
Date: Sun, 3 Jul 2011 22:53:39 -0700

Dear Dr Case
Thanks for your suggestion but i dont find the published paper
Im worry that the restraint limit vibrations in my system!
i try to solve my problem and ask you again

On Sun, Jul 3, 2011 at 5:47 AM, case <> wrote:

> On Sun, Jul 03, 2011, e p wrote:
> > I want to put a ligand in protein but I dont want to limit the
> vibrations.
> > I want to compare vibrations of atoms in active site in native enzyme and
> > mutants.
> > I can use rk2=5 or rk2=50 but I dont know which one is better?
> > Are the dist restraint in residues of active site in atoms that dont role
> in
> > mechanism or the restraint be in residues that dont in active site?
> > i dont want that ligand rotate or exit.
> > what is rotation restraint?is this help me or dist restraint is enough?
> Questions like the above don't have general answers. Without knowing
> anything
> about the nature of the protein and the ligand, and what kinds of distance
> restraints you are using (and how many), no one can help.
> Don't be afraid to experiment. If you want to "compare vibrations" it
> sounds
> like you would most likely want to use unconstrained simulations. Using
> artificial restraints to prevent the ligand from rotating or exiting might
> sometimes be useful, but you are probably going to have to run many
> simulations to get a feel for the effects of restraints.
> A good strategy is to find a published paper that does an analysis similar
> to
> the one you want to do, and use the procedure as a starting point.
> ....dac
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Received on Sun Jul 03 2011 - 23:00:03 PDT
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