I see. Thank you.
Wei
On Wed, Sep 10, 2014 at 5:57 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 10 2014 - 15:30:03 PDT
