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
> > > > _______________________________________________
> > > > 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
> _______________________________________________
> 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
Received on Sun Apr 10 2011 - 10:00:03 PDT
