Hi Qiong,
I'm forwarding this to Qin to see whether this has been resolved in
Amber12/AmberTools ...
Ray
---------- Forwarded message ----------
From: Qiong Zhang <qiong.zhang.qzh.gmail.com>
Date: Mon, May 14, 2012 at 2:48 PM
Subject: Fwd: Bug? Zero decomposed vdw and ele energies for explicit
water molecules in the decomposed PB calculation.
To: ray.luo.uci.edu
Dear Prof. Luo,
Sorry that the files may not be attached in the previous mail. Here
are they. Great thanks!
Qiong
---------- Forwarded message ----------
From: Qiong Zhang <qiong.zhang.qzh.gmail.com>
Date: Mon, May 14, 2012 at 2:45 PM
Subject: Bug? Zero decomposed vdw and ele energies for explicit water
molecules in the decomposed PB calculation.
To: AMBER Mailing List <amber.ambermd.org>
Hi All,
I am using amber11/ambertools1.5 and found a problem with per-residue
decomposed PB energies when explicit water molecules were included in
the analyses.
The problem is that when explicit water molecules are included in the
per-residue decomposed PB calculation, the decomposed vdw and ele
energies for those explicit water molecules are all zero. I tested
this on several different systems with explicit waters, this problem
existed in all cases.
Attached are the results from a decomposed PB calculation for a simple
system- a ligand and 35 water molecules. In decomp-pbsa.dat, it is
found that vdw and ele energies for explicit water molecules are all
zero. pb-decomp-result.dat is the FINAL RESULT from the decomposed PB
calculation and pb-result.dat is the FINAL RESULT from the normal
non-decomposed PB calculation. The total energies and binding free
energies in pb-decomp-result.dat are very close to those in
pb-result.dat, which indicates that the input files for the
per-residue decomposed PB calculation are correct.
Then why the decomposed vdw and ele energies for those explicit water
molecules are all zero in decomposed PB calculations please? Is it a
bug? In addition, decomposed GB values are all OK for the included
explicit water molecules.
Could you please give me some suggestions on this issue please? Thanks a lot!
Qiong
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Received on Mon May 14 2012 - 15:30:04 PDT
