Dear Prof Luo,
Thankyou the email, I hope that I will use the patch soon, that you are working on.
Thankyou very much for your time and considering my problem.
regards
Abhi
Date: Fri, 19 Dec 2014 15:48:03 -0800
From: "Ray Luo, Ph.D." <ray.luo.uci.edu>
Subject: Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna
To: AMBER Mailing List <amber.ambermd.org>, Abhishek TYAGI
<atyagiaa.connect.ust.hk>
Message-ID:
<CALRp-wonBuxy4dvROg0TJ37wa8=X65H9yUwRc+VViByyM=-mUw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Abhi,
Okay, it turns out that sander is trying to proceed with the PB
calculation even if ipb is set to zero because the good old flag igb =
10 is also used in the sander force() driver.
The ipb flag has been set to zero, i.e. bypassing PB, when the
initialization routine cannot detect a single charge in the system.
I'll submit a patch to reset igb value as well so PB won't be
triggered.
Thanks a lot for reporting! While I'm working on the patch, you can
safely set all electrostatic energies and PB/GB energies to zero for
the identically neutral receptor.
All the best,
Ray
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
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Received on Sat Dec 20 2014 - 23:00:02 PST
