[AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Wed, 07 Mar 2012 17:23:32 +0100


Within an MMPBSA analysis for a complex comprised of a charged receptor
and a charged ligand, I would like to use a non-linear PB solver.

I am using MMPBSA.py (of AmberTools 1.5), which itself is using PBSA in
order to derive the electrostatic energy of solvation. As MMPBSA.py has
no input variable that allows for selection of linear or non-linear
solver, I did the following:

1) call to MMPBSA with -make-mdins
2) sed -ie 's/npbopt = 0/npbopt = 1/g' _MMPBSA_pb.mdin
3) call to MMPBSA with -use-mdins

The third step fails with the following output:

   calculating complex contribution...
  PB Info in pb_read(): npopt has been overwritten with inp
  PB Info in pb_read(): eneopt has been reset to be 1 for nonlinear PB
  PB Bomb in pb_read(): cutnb=0 cannot be used with eneopt=1

MMPBSA.py, I believe, evaluates the energy "EEL" of the PBSA output. For
eneopt=2 (default), this -- according to the AT manual -- is "the
Coulombic energy". Now, the output above indicates that eneopt=1 is
enforced in case of the non-linear solver. In this case, EEL "includes
both the reaction field energy and the Coulombic energy".

Does it make sense to evaluate this kind of EEL in terms of MMPBSA? If
it does, besides changing npbopt in _MMPBSA_pb.mdin I also have to set
cutnb to a positive value. Which values would make sense?

Thanks for your help!


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Received on Wed Mar 07 2012 - 08:30:03 PST
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