hi all
I'm using Amber 11 and Ambertool 1.5. I noticed that my binding free energy
calculated from MMPBSA is different when I'm doing pb energy decomposition
or not. (This does not happen with gb) I further compared each energy terms
and found out that what makes the difference here is the "EPB" term
particularly for the receptor and complex.
I'm using ff10 and I added the old param for the Mg since I have that in
the system. This is the input I used for energy decomposition.
&general
startframe=1601, endframe=2000, interval=2,
keep_files=2,strip_mask=':WAT:Mg+:Na+',
/
&pb
istrng=0.100,
/
&decomp
idecomp=3, dec_verbose=1, print_res="3; 20-21; 23-27; 71-74; 85-87; 97;
102-110",
/
I suspect it's the Mg but then gb calculations were fine. Any idea? Thanks.
Victor
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Received on Tue May 08 2012 - 12:00:03 PDT
