AMBER Archive (2007)

Subject: AMBER: MMPBSA-nmode .top question

From: Matthew Danielson (mldaniel_at_pharmacy.purdue.edu)
Date: Fri Jun 15 2007 - 16:11:52 CDT

I am trying to compute a free energy of binding of a ligand to a large
protein using mmpbsa and nmode analysis with Amber 9.
        My question is that i see in many publications that a 10-15A region of
the system is cut out around the ligand, and the subsystem used to
obtain an estimate of dS. How is this done using amber? Is there a way
to tell the leap program not to add hydrogens to the termini when
generating a .top file? There will be many segments when the region is
cut, and I do not want amber to patch the termini with hydrogens as the
added atoms will not match the coordinates of the trajectory file I have
previously created.
        Any suggestions on generating the new .top file for the subsystem
without introducing extra atoms?

Thanks,
Matt Danielson

Purdue University
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