Re: [AMBER] MMPBSA

From: Ray Luo, Ph.D. <ray.luo.uci.edu> Date: Tue, 27 May 2014 12:41:24 -0700

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, May 27, 2014 at 11:05 AM, Hallel Freedman <hfreedma.ualberta.ca> wrote:
> Dear AMBER helplist,
> I have been trying to use MMPBSA and I keep getting this error:
>
> CalcError: /global/software/amber/amber13/bin/mmpbsa_py_energy failed with
> prmto
> p ../leapdir/complex.top!
> PB Bomb in pb_aaradi(): No radius assigned for atom           7 CB  C8
>
> I know that there has been discussion on similar problems in the past, but
> it was hard for me to understand for mreading these what the best fix is
> for this problem.
> I used the ff12SB force field to create my topology files.
> Thanks,
> Holly
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