Dear Amber users,
I am using Amber 9.0 for simulation. Using *ANAL* utility
in Amber I am trying to see the electrostatic interaction energy between the
two groups, say 1 and 2, contains residues which are not bonded to each
other. Anal will output the electrostatic energy matrix as shown below,
which is a sum of both 1-4 and non bonded interaction.
********************************************************************************************************************************************
ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX
1 2 3
1 -510.214 -120.865 -286.239
2 -120.865 4.281 31.622
3 -286.239 31.622 18.220
********************************************************************************************************************************************
Is it right to include the 1-4 electrostatic interaction if I want to see
the interaction energy between two non-bonded groups? Is there any other way
to see just the non bonded interaction alone?
Thanks in advance
Sincerely
Aneesh
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 08 2010 - 05:00:05 PST
