Dear Jason,
Thanks very much for you detailed explanation. Right now I think that I
know the reasons for the differences. Thanks!
So in order to get a reasonable result, what kinds of suggestion will you
give when doing mm/pbsa calculations, especially for choosing python
version? Thanks!
Best Regards,
Qinghua
On Sun, Dec 18, 2011 at 12:32 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> I'll try to outline some differences below:
>
> On Fri, Dec 16, 2011 at 5:21 PM, Qinghua Liao <fantasticqhl.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > Here are the results of the binding energy calculated by python and perl
> > mm/pbsa respectively, and also the input files are showed here.
> >
> > the input file for calculation of perl version:
> >
> > .GENERAL
> > VERBOSE 0
> > PARALLEL 8
> > #
> > PREFIX snapshot
> > PATH ../snapshots/
> > START 1
> > STOP 400
> > OFFSET 1
> > #
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > #
> > COMPT ../com.prmtop
> > RECPT ../rec.prmtop
> > LIGPT ../lig.prmtop
> > #
> > GC 0
> > AS 0
> > DC 0
> > #
> > MM 1
> > GB 1
> > PB 1
> > MS 1
> >
>
> Note that MMPBSA.py does not have molsurf (MS 1), so this will cause some
> differences.
>
>
> > #
> > NM 0
> > #
> >
> >
> ################################################################################
> > .PB
> > #
> > PROC 2
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 2
> > LINIT 1000
> > PRBRAD 1.4
> > ISTRNG 0.10
> > RADIOPT 1
> > INP 1
> > #
> > SURFTEN 0.00542
> > SURFOFF -1.008
> > #
> > IVCAP 0
> > CUTCAP -1.0
> > XCAP 0.0
> > YCAP 0.0
> > ZCAP 0.0
> > #
> >
> >
> ################################################################################
> > .MM
> > #
> > DIELC 1.0
> > #
> >
> >
> ################################################################################
> > .GB
> > #
> > IGB 5
> > GBSA 2
> > SALTCON 0.10
> > EXTDIEL 80.0
> >
>
> MMPBSA.py does not give direct access to EXTDIEL. The default in MMPBSA.py
> is 78.3, not 80 (which is the default value set in sander). We use the
> default and don't allow it to be changed too easily because the GB models
> here were parametrized to match PB results with those specific values of
> extdiel and intdiel.
>
> Also, some of the PB defaults are slightly different, I think (for
> instance, I think fillratio is different in the 2 programs for the
> MMPBSA.py input you gave).
>
> If you really want to compare them with the same input parameters, use the
> "use_sander=1" variable in MMPBSA.py and compare the _MMPBSA_gb.mdin file
> with the corresponding sander input file generated by mm_pbsa.pl.
> MMPBSA.py will actually give you the option of using a customized
> _MMPBSA_gb.mdin (or _MMPBSA_pb.mdin) via the -use-mdins flag. So you can
> tweak the MMPBSA.py input files to match the mm_pbsa.pl input files, which
> should give you an answer that matches to the precision used by the
> coordinate files.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Tue Dec 20 2011 - 02:00:03 PST
