Hello,
IÄm trying to analyze the output file of a pairwise decomposition run
with MMPBSA.py. My input file is this:
Input File for running GB
&general
startframe=4750,
endframe=5000,
interval=1,
keep_files=0,
/
&gb
igb=5,
saltcon=0.100,
/
&decomp
idecomp=3,
print_res="33-38; 41; 149; 152-153; 176-183; 204"
dec_verbose=3,
/
In all tables in FINAL_DECOMP_MMPBSA.dat, there are two energies for
each residue pair, e.g.
ASN 33 | ARG 41 ...
and
ARG 41 | ASN 33 ...
The values in these lines from the same table (e.g. complex, total
energy decomposition) are more or less similar, but not always exactly
the same, e.g. from complex sidechain energy decomposition:
Resid 1 | Resid 2 | Internal | van der Waals |
Electrostatic | Polar Solvation | Non-Polar Solv. |
TOTAL
ASN 33 | ARG 41 | 0.000 +/- 0.000 | -0.656 +/- 0.173 | -2.312
+/- 3.191 | 1.950 +/- 2.682 | -0.151 +/- 0.040 | -1.169 +/- 4.172
ARG 41 | ASN 33 | 0.000 +/- 0.000 | -1.183 +/- 0.315 | -4.760
+/- 3.185 | 3.822 +/- 2.655 | -0.316 +/- 0.033 | -2.437 +/- 4.159
My question is if these two values are supposed to be the same/similar
energies, and the difference stems form uncertainties/variance in the
calulation, or if the total pairwise energy is the sum of these two, and
how they are split.
Thanks,
Chris
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Received on Mon Apr 04 2011 - 07:30:06 PDT
