Are there any error or warning messages in any of the output files,
specifically either the standard error file, or in any of the _MMPBSA_*mdout
files?
-Bill
On Mon, Jun 13, 2011 at 6:25 AM, <zw258.cam.ac.uk> wrote:
> Jason Swails wrote:
> > Ah, it appears as though nab cannot handle a chamber-created topology
> file,
> > which makes sense. The CHARMM-specific potential terms are not coded
> into
> > nab.
> >
> > To fix this, you *must* have Amber11, and put the variable "use_sander=1"
> > in
> > your MMPBSA.py input file.
> >
> > Does this work?
> >
> > All the best,
> > Jason
> >
> >
> Hi Jason,
> "use_sander=1" seems worked until I got this "Segmentation fault". Any
> suggestions?
> ******************************
> Beginning GB calculations with sander...
> calculating complex contribution...
> calculating receptor contribution...
> Segmentation fault
> Error: sander error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
> make: *** [cal] Error 1Beginning GB calculations with sander...
> **********************************
>
> Best,
> Zhi
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Jun 13 2011 - 04:00:03 PDT
