AMBER: MM binding energy with ANAL

From: Ben Cossins <bcc.soton.ac.uk>
Date: Tue, 14 Sep 2004 13:56:37 +0100

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
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