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
>
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- application/octet-stream attachment: mmpbsa.in
Received on Sat Mar 12 2011 - 08:00:02 PST
