Hi Prof. Luo, Dr Cai and all,
I did two more simple tests with only 1 water and 2 water molecules.
For a system with only 2 water molecules, the decomposed PBSA result is as
follows:
| Run on Tue May 15 04:19:35 CEST 2012
idecomp = 2: Decomposition per-residue adding 1-4 interactions added to EEL
and VDW.
DELTAs can only be printed with the default mask assignments
Energy Decomposition Analysis (All units kcal/mol): Poisson Boltzmann
solvent
Complex:
Total Energy Decomposition:
Residue | Internal | van der Waals | Electrostatic
| Polar Solvation | Non-Polar Solv. | TOTAL
-------------------------------------------------------------------------------------------------------------------------------------------
WAT 1 | 1.622 +/- 0.000 | 0.000 +/- 0.000 | 0.000 +/- 0.000
| -9.324 +/- 0.000 | 0.000 +/- 0.000 | -7.702 +/- 0.000
WAT 2 | 1.672 +/- 0.000 | 0.000 +/- 0.000 | 0.000 +/- 0.000
| -8.951 +/- 0.000 | 0.000 +/- 0.000 | -7.279 +/- 0.000
Again *the vdw and elec components are zero for each water molecule in
decomposed PBSA.* The decompsed energies for water molecule in decomposed
PBSA (for systems with more than one water molecules) are close to those of
one single water molecule system, for which the vdw and elec components are
indeed zero.
But* the decomposed GBSA results look all OK*.
| Run on Tue May 15 04:23:02 CEST 2012
idecomp = 2: Decomposition per-residue adding 1-4 interactions added to EEL
and VDW.
DELTAs can only be printed with the default mask assignments
Energy Decomposition Analysis (All units kcal/mol): Generalized Born solvent
Complex:
Total Energy Decomposition:
Residue | Internal | van der Waals | Electrostatic
| Polar Solvation | Non-Polar Solv. | TOTAL
-------------------------------------------------------------------------------------------------------------------------------------------
WAT 1 | 1.622 +/- 0.000 | 27.097 +/- 0.000 | -5.080 +/- 0.000
| -9.405 +/- 0.000 | 0.605 +/- 0.000 | 14.839 +/- 0.000
WAT 2 | 1.672 +/- 0.000 | 27.097 +/- 0.000 | -5.080 +/- 0.000
| -9.453 +/- 0.000 | 0.557 +/- 0.000 | 14.793 +/- 0.000
Could you please direct me to some reference on the theoretical detail of
the MMPBSA per residue decomposition method implemented in Amber please?
Thanks!
Qiong
On Mon, May 14, 2012 at 6:00 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> 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
>
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Received on Mon May 14 2012 - 20:00:03 PDT
