AMBER: restrained md and mm pbsa

From: Christopher Gaughan <>
Date: Thu, 2 Aug 2007 10:15:17 -0400

Dear all,

I have been using mm-pbsa to calculate delta G of binding for a dimer of 2
28aa alpha helices. Thus far the error for these dG calculations has been
very high. I suspect it is because the dimer has overhangs on each side (ie.
the dimer is staggered not blunt ended). Thus there is a greater amount of
conformational freedom for the ends as compared to the central region which
is in contact with its counterpart. I wish to put restraints on the
overhanging regions. Will this adversely affect the final delta G of binding

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Received on Sun Aug 05 2007 - 06:07:27 PDT
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