---------- Forwarded message ----------
From: juan zeng <azengjuan.gmail.com>
Date: 2011/4/7
Subject: parameter about pbsa for sander
To: AMBER Mailing List <amber.ambermd.org>
Dear amber users:
Recently I calculated the binding free energy of my complex with
mm_pbsa.plin amber11,But the results comparing with that of others is
not expected.And
the main difference is the electrostatic energy section of the desolvation
free energies.I wonder if the parameters in my calculation are not
appropriate,So can you give me some advices which values of these parameters
should be adopted.By the way, If you can give me your parameters' values in
the process of your calculation,I will appreciate you very much.The
following text is my parameters:
File generated by mm_pbsa.pl. Using PB
&cntrl
ntf = 1, ntb = 0,
ipb = 2, inp = , dielc = 1.0,
cut = 999.0, nsnb = 99999,
imin = 1, maxcyc = 0, ntmin = 2,
ivcap = 0, cutcap = -1,
xcap = 0, ycap = 0, zcap = 0
idecomp= 0,
&end
&pb
epsin = 1.0, epsout = 80.0,
istrng = 0.0, radiopt = 0,
sprob = 1.4, space = 0.5,
maxitn = 1000, dbfopt = 1,
cavity_surften = 1.0, cavity_offset = 0.0,
npbverb= 1
&end
Best wishes
Juan.
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Received on Thu Apr 07 2011 - 08:00:03 PDT
