[AMBER] MMPBSA.py EPB problem with idecomp=3

From: Ryan Pavlovicz <pavlovicz.7.osu.edu>
Date: Thu, 5 Sep 2013 19:17:02 -0400


I recently performed a set of MMPBSA calculations with MMPBSA.py.MPI
(AmberTools 13, patches update.1-update.14 applied) using idecomp=1 with
good results. I then attempted to perform a pair-wise decomposition on the
same data set using idecomp=3 and noticed inconsistent EPB results.

The -o output (which i wouldn't expect to be affected by the idecomp
setting) was nearly identical for all components of the two calculations
except for the EPB values.

Here are the input parameters:


    endframe=4000, verbose=2, keep_files=2, debug_printlevel=2,
   istrng=0.150, inp=1, cavity_offset=0.92, cavity_surften=0.00542,
   idecomp=1, print_res="1-257"


   startframe=1, endframe=4000, verbose=2, keep_files=2, debug_printlevel=2,
   istrng=0.150, inp=1, cavity_offset=0.92, cavity_surften=0.00542,
   idecomp=3, print_res="58,61-62,65-66,69,74-75,79-84,86-87,92,232-257"

And some of the -o output averages for the complex energies:

from INPUT1 calculation:

BOND 767.3825
ANGLE 2123.0202
DIHED 1591.6132
VDWAALS -2048.7067
EEL -17663.9213
1-4 VDW 956.6694
1-4 EEL 9456.6797
EPB -2936.0288
ENPOLAR 71.5819

form INPUT2 calculation:

BOND 767.3857
ANGLE 2123.0294
DIHED 1591.6116
VDWAALS -2048.7072
EEL -17663.9226
1-4 VDW 956.6795
1-4 EEL 9456.6795
EPB -1.6261
ENPOLAR 71.5807

In all five sets of calculation i performed, the EPB values for the
idecomp=3 simulations were very small compared to those obtained from the
idecomp=1 simulations. Maybe someone can spot an error in my inputs or
identify this as a bug in the MMPBSA.py code.

If this is a bug, i assume that the pair-wise Polar Solvation terms may
also not be correct. They all seem fairly small in my -do files (ranging
from about -1 to 1), although i'm not sure how small they should be when
broken down pair-wise.

Any help would be much appreciated.


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Received on Thu Sep 05 2013 - 16:30:02 PDT
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