Dear Dr. Bill
Thanks again for your kind interest.
I recalculated the binding energy again using the method you have described, but I got the same answer.
I observed that the difference is only in Ggas (i.e. VDW and ELE). But the GB value is the same for both calculations. I believe my results are liable where the final binding energy is the same for the both calculations.
I am now trying to patch all the bugfix available, it may be a reason.
On any way, I wanted to thank you.
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, 3:47 PM
> 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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> _______________________________________________
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> > > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Mar 12 2011 - 10:30:02 PST
