Hi Jason,
Option 1 doesn't seem to work because, this way, I calculate positive large
values of deltaG. I haven't tried option 2 yet.
As far as option 3, I would like to try it, but because I am running on
many ligands, I need to use parmed.py instead of xparmed.py. Would you mind
giving me an example please of what I would write in parmed for this?
Thanks,
Holly
On Thu, May 29, 2014 at 1:07 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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 - 13:00:02 PDT
