Re: [AMBER] QUESTION ON MMPBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 10 Apr 2011 10:53:02 -0700

Are you talking about the tutorial? The final results file can be
downloaded in several locations on the tutorial site, it's not necessarily
included in the zip files (I don't remember exactly where they are).

If you're talking about no FINAL_RESULTS_MMPBSA.dat file appearing after
you've run the sample calculation, we can't help without more information.
The only reason it wouldn't print a final results file is if something went
wrong, in which case we'd need the error message that was generated.

All the best,
Jason

On Sun, Apr 10, 2011 at 9:55 AM, vani panguluri <vanipanguluri.gmail.com>wrote:

> I got the MMPBSA files but i am not able to found the finalresults.dat file
> in my output. can i know why it so happening.........
>
> Regards,
> Vani
>
> On Fri, Apr 8, 2011 at 1:01 PM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > In this calculation, mmpbsa.in, 1err.solvated.prmtop, complex.prmtop,
> > receptor.prmtop, ligand.prmtop and all files that end in .mdcrd are input
> > files for this calculation. Everything except mmpbsa.in can be found in
> > that
> > zip file that I mentioned previously.
> >
> > -Bill
> >
> > On Fri, Apr 8, 2011 at 1:48 PM, vani panguluri <vanipanguluri.gmail.com
> > >wrote:
> >
> > > in this the complex ,receptor and ligand are our input files or else we
> > > need
> > > to consider those files also from these Zip files.
> > >
> > > Regards,
> > > Vani
> > >
> > > On Fri, Apr 8, 2011 at 12:15 PM, Bill Miller III <
> brmilleriii.gmail.com
> > > >wrote:
> > >
> > > > All of these files can be downloaded from Section 3.2 of the online
> > > > tutorial
> > > > (
> > http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
> > > ).
> > > > All of the files necessary to run this MMPBSA.py calculation can be
> > > > downloaded on that site as part of the tarball near the top of the
> page
> > > > called Est_Rec_top_mdcrd.tgz.
> > > >
> > > > I hope that helps.
> > > >
> > > > -Bill
> > > >
> > > > On Fri, Apr 8, 2011 at 1:01 PM, vani panguluri <
> > vanipanguluri.gmail.com
> > > > >wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > In the MMPBSA.PY in protein- ligand complex how can I get the
> > > > > *1err.solvated.prmtop
> > > > > that *file i had done the prod steps as shown in the manual but i
> got
> > > > > stucked over this step
> > > > > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> > FINAL_RESULTS_MMPBSA.dat
> > > > -sp
> > > > > 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> > > > > ligand.prmtop -y *.mdcrd
> > > > >
> > > > > Can anyone explain me in detail about this step and how to get
> those
> > > > files
> > > > >
> > > > > Regards,
> > > > > Vani
> > > > > _______________________________________________
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Bill Miller III
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-6715
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> > > >
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> > >
> >
> >
> >
> > --
> > 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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>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Apr 10 2011 - 11:00:02 PDT
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