Re: [AMBER] mmpbsa: PB Bomb in pb_aaradi()

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 10 Sep 2014 14:57:56 -0700

Wei,

Indeed, it can't recognize these new atom types. We are working on a
new set of PB radii with updated explicit water models. In the
meantime, please use radiopt=0, i.e. the mbondi as provided in LEAP.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Sep 10, 2014 at 2:18 PM, Wei Chen <cwbluesky.gmail.com> wrote:
> Hello,
>
> I am using AmberTools14 for MMPBSA calculation. The force field is ff12SB.
>
> My input for pb is:
> &pb
>    istrng=0.15, prbrad=1.4, radiopt=1, inp=2,
>    indi=1.0, exdi=80.0, sander_apbs=0, scale=2.0,
>    cavity_surften=0.0378, cavity_offset=-0.5692
> /
>
> I got this error:
> "PB Bomb in pb_aaradi(): No radius assigned for atom     7  CB    2C".
>
> It is a CB atom in a standard amino acid. I saw somebody asked the same
> question before. The program cannot recognized the atom type "2C". I think
> many people are using ff12SB force field now. I wonder why regular atom
> types in ff12SB cannot be recognized. Is that because the optimized radii
> set obtained by using other force field, thus not suitable for ff12SB?
>
> Thank you!
>
> Wei Chen
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Received on Wed Sep 10 2014 - 15:00:03 PDT
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