AMBER Archive (2004)

Subject: AMBER: Decomposition in MMPBSA

From: Thomas Steinbrecher (
Date: Thu May 13 2004 - 19:15:03 CDT

Dear AMBER users,

I try to figure out the contribution of different aminoacids to the
binding free energy of a protein ligand complex using the decomp parameter
in mm_pbsa with amber8.

My decomp section of the input file is:

COMREC 1-218
COMLIG 219-219
COMPRI 170-180 219-219
RECRES 1-218
RECPRI 170-180
RECMAP 170-180
LIGMAP 219-219

This gives me lines like this as in the *.all.out files:

TDC 170-> 170 0.000 -1.382 -14.482 -4.133 917.642
TDC 170-> 171 0.000 -0.312 -25.515 -0.344 -93.099

So this is the interaction of residue 170 with itself and with residue
171. I suppose the other five numbers are INT ELE VDW GBSOL and GBSUR but
I'm not sure in which order. I couldn't find this information in
the manual (amber8) or searching for decomp in the archives. I tried to
read the code, but my perl-skills don't seem to suffice here.

I wonder where the huge positive number at the end of the first line
comes from and I'm curious how the pairwise interaction energy of a
residue with itself is computed, because I expected the total
interaction energy of the ligand with itself to be the same as the total
free energy of the ligand when running mm_pbsa without decomposition,
though that was not the case.

I also noticed that the interaction of each possible pair of residues is
computed. I am only interested in the interaction of the ligand with
the different aminoacids, is there a way to compute only these
interaction pairs in mm_pbsa? I know that anal was supposed to be used
for that, but it's no longer supported.

Also the interaction between e.g. resid 170 and 171 is calculated as well
as the interaction of resid 171 and 170. Is there any situation where
these two values can be different?

Thanks in advance for any comments,

Kind Regards,

Thomas Steinbrecher

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