MMPBSA.py has undergone some modification since the release of AMBER 11.0,
and 'nmode_igb' is one of the new additions. You can download the latest
release of MMPBSA.py from the tutorial installation page (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm). The
installation instructions are on that same website. Also, don't forget to
download and apply the patches for MMPBSA.py on that same page.
Good luck!
-Bill
On Tue, Jul 20, 2010 at 11:24 AM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> Hi,
> recently i started using MMPBSA.py script in Amber 11.0. I am doing
> entropy calculation using normal mode analysis, as described in AMBER
> ADVANCED TUTORIALS
> TUTORIAL 3 - SECTION 3.5,
> ------------------input file -----------------------
>
> Input file for running entropy calculations using NMode
> &general
> endframe=50, keep_files=2,
> /
> &nmode
> nmstartframe=1, nmendframe=50,
>
> nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> /
>
>
> -------------------------------------------------------------------------------------------------------
>
> But calculation are finishing with "Warning: Input error! "nmode_igb=1" is
> an invalid option." i tried to grep this variable in amber code but i
> couldnot find it. Please can u write me that whats the issue exactly ?? is
> this vatiable being use in updated release of MMPBSA.py, which is after
> release of amber 11.0 ?
>
> Sincerely
> ..Sus
> _______________________________________________
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> 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
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Received on Tue Jul 20 2010 - 09:00:03 PDT
