Is there a Mg in the receptor or ligand prmtop files? You have specifically
stripped out the Mg ion in the input file (strip_mask=':WAT:Mg+:Na+') so
there should not be any Mg ions in the dry complex, receptor, or ligand
trajectories that are created by MMPBSA.py and analyzed. So if you have a
Mg in any of those corresponding prmtop files, that would create a
discrepancy between the prmtop and the coordinates. You also may want to
upgrade to AmberTools12. I think the updates for MMPBSA.py would catch this
inconsistency before the calculation.
I hope that helps.
-Bill
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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 08 2012 - 12:00:04 PDT
