Re: [AMBER] dist restraint

From: case <>
Date: Sun, 3 Jul 2011 08:47:39 -0400

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.


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Received on Sun Jul 03 2011 - 06:00:03 PDT
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