On Thu, May 29, 2014 at 2:34 PM, Hallel Freedman <hfreedma.ualberta.ca>
wrote:
> OK, but unfortunately I still get the same error message:
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB C8
>
> when I run the serial program.
>
Previous discussions (e.g.,
http://archive.ambermd.org/201208/0074.html)
suggest the cause.
Make sure you are using the latest version of AmberTools, but the things
you should try are:
1) Set inp=1 and radiopt=0 in the &pb section of your MMPBSA.py input file
2) Keep the default value of inp and set radiopt=0 in the &pb section of
your MMPBSA.py input file
3) Use the ParmEd trick described in the thread linked above.
Personally I would do #1 to use the simple nonpolar solvation model.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 29 2014 - 12:30:02 PDT
