Dear amber users,
I am running mm_pbsa calculation for two MD simulation results for the same
system to obtain binding energy information between ligand and protein. One
MD simulation consider all system (protein+ligand+water box) and another
simulation only consider active site proteins and the atoms within 20 A of the
active site proteins (with the other atoms fixed during the MD simulation).
The mm_pbsa calculated binding energy for the full sys is -161 +/- 14 kcal/mol
and the binding energy for the other system is -168 +/- 14 kcal/mol. Are
these values reasonable good for two same system with different MD treatment?
Another question, the calculated absolute energy for these two system is total
different. In full system, the average calculation energy for protein, ligand
and complex (protein+ligand) are -7456, -120 and -7745, respectively.
In another system, the average calculation energy for protein, ligand and
complex (protein+ligand) are 174491, -15, 174309, respectively. I am not
quite sure what cause the absolute energy so different. Is there any
suggestion? Thanks in advance.
Wentao Fu
Ctr. Pharm. Biotech.
University of Illinois at Chicago
Received on Mon Nov 19 2001 - 15:32:14 PST
