To add on to what Bill said, the version included in Amber11 does NOT
contain decomposition, the version he linked to in his response does.
Future versions will contain a version number to eliminate this ambiguity,
and installation will be greatly improved/made easier.
Good luck!
Jason
On Wed, Nov 10, 2010 at 3:18 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> How old is your version of the MMPBSA.py? I do not believe decomp was
> supported in the earlier releases of MMPBSA.py. However, if you download
> the
> updated source code the from tutorial website (
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/) and re-compile
> mmpbsa_py this should fix this error. Don't forget to apply the patches to
> the source code, which can also be found on the website.
>
> Good luck!
>
> -Bill
>
> On Wed, Nov 10, 2010 at 3:09 PM, <kbarakat.ualberta.ca> wrote:
>
> > Hello,
> >
> > I'm running energy decomposition for my system. I'm using this input
> > file (see below), however the python script doesn't recognize the
> > &decomp keyword. Do I miss something. Sorry, I'm new to this script.
> >
> > Thanks,
> > Khaled
> >
> > Input file
> > &general
> > startframe=1, endframe=1000, interval=100,
> > keep_files=2, entropy=1,
> > /
> > &pb
> > istrng=0.15, fillratio=4.0
> > /
> > &gb
> > igb=2, gbsa=1, saltcon=0.150,
> > surften =0.0072, surfoff = 0.09,
> > /
> > &decomp
> > idecomp=1, print_res="1-237"
> > dec_verbose=1,
> > /
> >
> >
> >
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Nov 10 2010 - 14:00:02 PST
