AMBER: decomposition energy

From: Pankaj R. Daga <>
Date: Tue, 4 Sep 2007 09:31:25 -0500

Dear Amber Community,


I am running decomposition energy calculations for one protein-ligand
complex using mm_pbsa. The protein has 389 residues. The run went on fine.
Total GBTOTAL is same as that from binding energy calculation.


>From the data, it seems that the last residue no. 389 is contributing the
most (-34.8) in the total energy (-78.8), although this residue is far away
from active site. I am confused, how one residue can contribute almost 40%
of the binding energy, even if it is not a part of active site. I have
plotted the delta_energy results against residue number. I am attaching the
two plots, one with last residue included and the other with the last one
omitted. I am also attaching the final output file from DC run


Could you please tell me, if I am missing something in the data


Thanks and Regards




If your ship doesn't come in, swim out to it.......Jonathan Winters
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail:
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |


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Received on Wed Sep 05 2007 - 06:07:35 PDT
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