I think the PB decomposition and PB "normal" have a different set of
defaults. This could cause very different total free energies, but the
binding free energy should be pretty close (since the differences should be
largely conserved between the complex and receptor).
If I'm misinterpreting your issue, and you're getting a message like
WARNING: INCONSISTENCIES EXIST...
then Bill's response gives the appropriate advice.
A PBSA expert would have to comment more on the changes between decomp PB
and normal PB.
HTH,
Jason
On Tue, May 8, 2012 at 2:29 PM, Victor Ma <victordsmagift.gmail.com> wrote:
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 08 2012 - 12:00:06 PDT
