AMBER: ibelly and free energy calculations

From: David Mobley <>
Date: Mon, 12 Sep 2005 14:36:25 -0700


We're trying to do some free energy calculations (icfe=1) with ibelly=1
(with belly restraints). Particularly, I have calculated a variety of ligand
binding affinities with full protein flexibility by disappearing the ligands
from the binding pocket and doing the relevant thermodynamic cycle, and want
to try the same while holding the protein fixed (a belly simulation would be
a nice way to do this). However, I get an error from sander when I try to do
this: "ibelly cannot be used with icfe" and sander exits with an "input

Is there a fundamental reason why this can't work? Or has it just been
disabled in sander to prevent people from (for example) restraining atoms
which they are also perturbing, or some similar thing? In my case, this
wouldn't apply: I'm trying to restrain the protein while using TI to
disappear the ligand. Would it be safe to simply disable the warning and
recompile? Or are there other problems I'm not aware of?

David Mobley
Ken Dill group

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Received on Mon Sep 12 2005 - 22:53:00 PDT
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