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 - 12:00:03 PDT
