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
Received on Fri Apr 08 2011 - 11:30:04 PDT
