I have Mg in my system (not ligand) but as you mentioned they should all be
stripped out in MMPBSA calculation and dry complex, receptor files are both
Mg free. Also my gb calculations are consistent. So the "strip_mask" should
be fine.
So what else should I check? Thanks.
On Tue, May 8, 2012 at 1:35 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 08 2012 - 12:00:08 PDT
