Amber12 has the same problem, and there is a bug in the decomposition part.
Thanks for reporting, Qiong!
Best,
Qin
On May 14, 2012, at 5:00 PM, Ray Luo, Ph.D. wrote:
> 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
> <decomp-pbsa.dat><pb-decomp-result.dat><pb-result.dat>_______________________________________________
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Received on Wed May 16 2012 - 11:00:04 PDT
