Hello,
I am applying MMPBSA.py from AT 1.5 and AT 13 to the same set of
topologies and trajectory, yielding a free energy of binding of
- about 850 kcal/mol in case of AmberTools 13
- about -30 kcal/mol in case of AmberTools 1.5
This is due to a huge discrepancy in the non-polar terms:
delta ECAVITY (AT 1.5): -3.7 kcal/mol
delta ENPOLAR (AT 13) : 880.4 kcal/mol
I am working on a system with atom types not known by PBSA, so that's
why I use radiopt=0 & inp=1 for MMPBSA.py in AT 13. The input files:
AmberTools 13 MMPBSA.py
========================
Input file:
&general
verbose = 2,
/
&pb
#
http://archive.ambermd.org/201211/0319.html
radiopt=0,
inp=1,
/
AmberTools 1.5 MMPBSA.py
========================
Input file:
&general
verbose = 2,
/
&pb
/
Ray Luo once said about inp=1 "Okay, please set inp=1 in the &cntrl
namelist to recover the original behavior in Amber11", so I did not
expect this difference.
Both methods happily bring BOND, ANGLE, DIHED, VDWAALS, EEL, the 1-4
terms, and EPB into agreement.
The large difference actually comes from the discrepancy in the ECAVITY
/ ENPOLAR terms:
AT 1.5 ECAVITY:
- complex: 91.2709
- receptor: 89.6098
- ligand: 5.3839
- diff: -3.7228
AT 13 ENPOLAR:
- complex: -17162.3737
- receptor: -16853.4615
- ligand: -1189.3078
- diff: 880.3956
Much larger numbers here in case of AT 13. Is that expected behavior? Or
does something go wrong in the MMPBSA run with the inp=1 setting?
Cheers,
Jan-Philip
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Received on Tue Apr 30 2013 - 03:30:02 PDT
