AMBER: Res minimization

From: Thomas Leonard <>
Date: Tue, 15 Jul 2008 15:34:47 +0800 (SGT)


I am trying to minimize a ligand bound protein, in which the ligand always
comes out of the binding pocket during the minimization.

So tried res minimization. I wonder even in the res minimization the
ligand comes out of the pocket even with a high force constant of 500.

what is worng with my inputs
please advice

initial minimisation solvent + ions
imin=1, maxcyc=500,
Group input for restrained atoms
RES 88 90


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Received on Wed Jul 16 2008 - 06:07:31 PDT
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