AMBER Archive (2008)

Subject: AMBER: Res minimization

From: Thomas Leonard (thomasj_at_bii.a-star.edu.sg)
Date: Tue Jul 15 2008 - 02:34:47 CDT

Hi

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
&cntrl
imin=1, maxcyc=500,
 ntpr=5,
 ntr=1,
 &end
Group input for restrained atoms
500.0
RES 88 90
END
END

Thomas

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