AMBER: MM-PBSA calculations of entropy within the sphere

From: Sergey Samsonov <>
Date: Wed, 22 Aug 2007 15:49:25 +0200

Dear AMBERs,

in a number of articles (for examples: Wang et al. 2000; Kuhn, Kollman
2000; Weis et al 2006 etc) the authors used just part of the receptor
(the residues within certain cut-off from the ligand) for the MM-PBSA
calculations since this allowed to decrease the computational expenses
for very demanding entropy calculations. The question is: how to create
the proper topology files? If I use xleap I'd get the terminal atoms for
the cut residues, which, of course, are not present in my trajectory, so
I can't proceed in this way. Is it possible to cut the residues from
topology file in rdparm? I tried but I didn't find the appropriate
solution for this problem. The same question arised 3 years ago on the
list (it is stored in the archive under "AMBER: nmode with mm/pbsa"
topic) but it wasn't answered in details.

Thank you very much in advance for your help.

Best wishes,

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Received on Sun Aug 26 2007 - 06:07:10 PDT
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