Dear Amber community,
I have attempted to use ANAL to calculate the MM component of a binding
energy. I analysed two groups in ANAL one being the receptor atoms and the
other being the Ligand atoms. I took the computed Total INTER energy as the
MM binding energy, which as seen in the ouput below was -112.88.
input:-
ANAL in file what a crappy format
1 0 0 0 0 1
0 0.0 0.0 0.0 0.0
1 0 0 0 0 0
999.0 2.0 1.2 1.0
1 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0
ENERGY
Ligand
RES 341 341
END
Receptor
RES 1 340
END
END
STOP
output:-
TOTAL INTERACTION ENERGY MATRIX
1 2
1 106.318 -112.879
2 -112.879 -2758.950
INDIVIDUAL GROUPS INTERACTION
GROUP INTRA INTER TOTAL
1 106.32 -112.88 -6.56
2 -2758.95 -112.88 -2871.83
TOTAL -2652.63 -112.88 -2765.51
This gives different figures from those given by using mm-pbsa and therefore
sander to get figures for seperated Ligand , Receptor and Complex structures
and finding the difference. The comparable figure from mm-pbsa was -124.20.
should these figures be the same?
Thanks
Ben Cossins
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Received on Tue Sep 14 2004 - 14:53:01 PDT
