AMBER Archive (2007)

Subject: RE: AMBER: decomposition energy

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed Sep 05 2007 - 05:42:42 CDT

Dear Pankaj and amber users,
 
I am doubt if the GBtotal is the free energy or the enthalpy, as GBtotal did not take the TdeltaS into consideration? Am I correct?
 
Best regards,
 
Cat

From: pdaga_at_olemiss.eduTo: amber_at_scripps.eduSubject: AMBER: decomposition energyDate: 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 ˇ§snapshot_statistics.outˇ¨.
 
Could you please tell me, if I am missing something in the data interpretation?
 
Thanks and Regards
 
Pankaj
 
===================================================================If your ship doesn't come in, swim out to it.......Jonathan Winters===================================================================Pankaj R. Daga | Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638University of Mississippi | phone: +1-662-915-1853University, MS, 38677-1848 | ===================================================================
 
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