[AMBER] MMPSA: PB Bomb in pb_aaradi(): ...

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Tue, 07 Aug 2012 15:03:12 +0200

Dear Amber users,

We are trying to use MMPBSA (AMBER12 + AmberTools 12) to estimate the
binding affinity of a protein to DNA. However, when we try to use the
non-linear Poisson Bolzmann (npbopt=1) with the the non-polar solvation
free energy estimated using the cavity and dispertion terms approach
(inp=2), we are getting the error "PB Bomb in pb_aaradi(): No radius
assigned for atom 14 CG C6" (see details below). The atom is a CG in a
ASP (C6 atom type in the ILDN-modified ff99SB force field). Please see
details of the run below.

Now, if we use inp=2 and radiopt=0 (radii taken from the topology file;
we know we should not do this in principle - but we did it for testing),
the same error occurs.
However, if we use inp=1 and radiopt=0, MMPBSA runs but it gives
abnormal results (in the range of +4000 kcal/mol .. obviously a non-sense).
When we use inp=0 and radiopt=0, we get a better result (in the range of
-100 kcal/mol) but here we do not take into account the non-polar
solvation free energy
MMGBSA runs fine with the same system and gives reasonable values at
first glance (in the range of -200 kcal/mol).

Could anybody explain this error message? Are we doing something wrong
here ?

Also an additional question: how should we control the SASA calculation
in MMBSA ? ssaopt=0, saopt=0 are defaults. Does this mean that by
default no estimation of SASA is done since saopt=0? Does the gbsa
parameter play any role for MMPBSA or is used just for GB calculations ?

Than you very much for your comments on this?

Best wishes

##Command (AMBER12 + AmberTools 12)
mpirun -np 6 MMPBSA.py.MPI -i mmpbsa.in -o mmpbsa.out -cp complex.prmtop
-rp receptor.prmtop -lp ligand.prmtop -y complex.cdf -eo detail -use-mdins

File generated by MMPBSA.py
  nsnb=99999, dec_verbose=0, ipb=2,
  ntb=0, cut=999.0, imin=5, inp=2,
  istrng=150.0, maxitn=1000, npbopt=1,
  fillratio=4.0, radiopt=1, use_sav=0, cutnb=25.,

Energy minimization:
      maxcyc = 1, ncyc = 10, ntmin = 1
      dx0 = 0.01000, drms = 0.00010
  PB Bomb in pb_aaradi(): No radius assigned for atom 14 CG C6

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Tue Aug 07 2012 - 06:30:02 PDT
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