AMBER Archive (2008)

Subject: AMBER: ANAL

From: Madhumalar Arumugam (madhumalar_at_bii.a-star.edu.sg)
Date: Wed Oct 29 2008 - 03:44:57 CDT

Hello users,
  I am trying to use ANAL module of AMBER8 for getting the residuewise
interaction energy (vDW+elec) for a system of protein+ligand
and I used the following inputs,

 1 0 0 0 0 1
    0 0.0 0.0 0.0 0.0
    1 0 0 0 0 1
  10.0 2.0 1.2 1.0
    1 10.0 10.0 10.0 10.0 10.0 10.0 20.0 10.0 10.0
ENERGY
receptor
RES 1 88
END
ligand
RES 89 101
END
END
STOP

I got the output..which I couldn't understand.

 number of non-bonded residue pairs = 1899

individual pair energies greater than 10.00 kcal/mol

 NBOND 1- 1 HC( 1)-CT( 49) 2.094 12.176 -7.339
  NBOND 1- 1 HC( 1)-HC( 51) 1.484 63.673
2.512
  NBOND 1- 1 CT( 2)-HC( 51) 2.082 13.061
-5.839
  NBOND 1- 1 C ( 5)-C ( 17) 5.240 -0.024
30.477
similary for other types of energies vdw14, ele14. could anyone suggest me
which values I should take, for example vdw component of residue 1 with 2.
Also, I wonder how reliable these values are?

Thanks in advance for any info.

Madhu

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