AMBER: Newbie question: partial minimization in implicit solvent

From: Jochen Heil <>
Date: Wed, 12 Nov 2008 18:48:38 +0100


I have a protein pdb structure built from X-ray data with hydrogen atoms
added by some empirical/heuristical method. I want to perform a partial
optimization using a GB implicit solvent model by constraining the
positions of certain atoms (defined by groups or geometric criteria).

The obvious solution seems to be to construct an input similar to the
following (just an example for the optimization of hydrogen sites):

    imin=1, ntb=0, cut=999, igb=1, ibelly=1, bellymask=".H="

However, the manual says (Amber9/10) that GB implicit solvent minimization
using constraint atoms is currently not possible. On the other hand,
apparently allows the definition of frozen atoms upon GB minimization
in the context of amber_score. Is there a workaround for doing this in
native Amber?

Cheers, Jochen

Dipl.-Ing. Jochen Heil
AG Kast
Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
Technische Universität Darmstadt
Petersenstr. 20, 64287 Darmstadt, Germany
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Received on Fri Dec 05 2008 - 14:34:16 PST
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