To ensure that the exact same calculation is being performed, you should use
the -use-mdins flag for MMPBSA.py. Take the mdin file created by
mm_pbsa.pland change the imin (from 1 to 5) and surften (from 1.0 to
0.007s)
variables. Then take that mdin file and call it _MMPBSA_gb.mdin. Place it in
the directory you are doing analysis with MMPBSA.py. Then use the exact same
command you have been using for MMPBSA.py, but add -use-mdins at the end of
it.
This will ensure that all of the variables are exactly the same for both
MMPBSA.py and mm_pbsa.pl. This is how I have previously demonstrated that
mm_pbsa.pl and MMPBSA.py give the exact same results using the same input
files. I find this method easier than double and triple-checking every
single variable to be the same, as I normally make a mistake (or two or
three) doing this.
I hope that helps.
-Bill
On Sat, Mar 12, 2011 at 10:32 AM, Eliac Brown <eliacbrown.yahoo.com> wrote:
> Dear Dr. Bill
> Thanks so much for your reply.
> First, is mmpbsa.py decomp option working well with amber10? I see on the
> website, it is mentioned that it is available only with amber11
> Secondly, for the difference in the output, I am pretty sure as I believe
> the input files generated by the different scripts have the same parameters'
> value:
>
> File generated by MMPBSA.py
> &cntrl
> ntb=0, idecomp=0, cut=999.0, nsnb=99999,
> imin=5, maxcyc=1, ncyc=0, igb=2,
> saltcon=0.150, intdiel=1, extdiel=78.3, gbsa=1,
> surften=0.0072,
> /
>
> File generated by mm_pbsa.pl. Using MM GB MS
> &cntrl
> ntf = 1, ntb = 0, dielc = 1.0,
> idecomp= 0,
> igb = 2, saltcon= 0.15,
> offset = 0.09,
> intdiel= 1.0, extdiel= 78.3,
> gbsa = 1, surften= 1.0,
> cut = 999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
> imin = 1, maxcyc = 1, ncyc = 0,
> &end
>
> The full input and output files are attached
>
> Finally, thanks in advance
> Eliac
> --- On Sat, 3/12/11, Bill Miller III <brmilleriii.gmail.com> wrote:
>
> > From: Bill Miller III <brmilleriii.gmail.com>
> > Subject: Re: [AMBER] Energy Decomposition using mmpbsa script
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Saturday, March 12, 2011, 1:31 PM
> > If all the input variables are
> > exactly the same, then mm_pbsa.pl and
> > MMPBSA.py should give you the exact same answer for all
> > components. We made
> > sure this was the case when we wrote and released
> > MMPBSA.py. The difference
> > is that some of the variables have different defaults in
> > MMPBSA.py than the
> > suggested values in mm_pbsa.pl, such as igb.
> >
> > What are the lines in and surrounding line 358 of
> > AMBER-10.0/amber10/lib/mm_pbsa/mm_pbsa_readinput.pm ? Also,
> > could you post
> > your input file for mm_pbsa.pl?
> >
> > And have you tried decomposition analysis with MMPBSA.py?
> > Did that give you
> > any problems?
> >
> > -Bill
> >
> > On Sat, Mar 12, 2011 at 8:05 AM, Eliac Brown <eliacbrown.yahoo.com>
> > wrote:
> >
> > > Dear AMBER
> > > Firstly, I calculated the mmgbsa binding energy using
> > mmpbsa.pl and using
> > > mmpbsa.py, I got the identical final delta energies,
> > but the the energy
> > > components for each of ligand, receptor and complex
> > were different using the
> > > two mmgbsa scripts, is that normal? (not I used MS=0
> > to force the program to
> > > calculate the solvation using LCPO method as it is
> > done with pythone
> > > script).
> > > Secondly, I am trying to calculate the energy
> > decomposition using GB model
> > > (mmpbsa.pl) , if I specified PB = 0 it gives me an
> > error :
> > > AMBER-10.0/amber10/lib/mm_pbsa/mm_pbsa_readinput.pm
> > line 358
> > > when I change PB to 1, it works normally, but I don't
> > need to calculate PB
> > > where it is very expensive calculation. how can I do
> > that?
> > > Thanks in advance for your help
> > > Eliac
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
> _______________________________________________
> 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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Received on Sat Mar 12 2011 - 08:00:04 PST
