Dmitry,
It looks like that the input file is asking for radii to be read from the
prmtop file, so I don't know why the error message got printed. Can you
email me off the list the prmtop and a sample inpcrd file for us to
reproduce the problem? I suppose this is from the python script that calls
sander?
Ray
On Wed, Nov 14, 2012 at 10:21 AM, Dmitry Mukha <dvmukha.gmail.com> wrote:
> Hi Ray,
>
> an input file was following
>
> File generated by MMPBSA.py
> &cntrl
> ntb=0, igb=10, cut=999.0, nsnb=99999,
> imin=1, maxcyc=0, cutcap=-1, xcap=0,
> ycap=0, zcap=0, idecomp=0, ntpr=1,
> ivcap=0, ntmin=2,
> /
> &pb
> dbfopt=1, epsin=1, epsout=80, istrng=150.0,
> radiopt=0, sprob=1.4, space=0.5, maxitn=1000,
> npopt=1, cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4,
> /
>
> Any your suggestions?
>
> Best regards,
>
> Dmitry
>
>
> 2012/11/14 Ray Luo, Ph.D. <ray.luo.uci.edu>
>
> > What's the input file generated for pb calculations?
> >
> > Ray
> >
> > On Wed, Nov 14, 2012 at 12:52 AM, Dmitry Mukha <dvmukha.gmail.com>
> wrote:
> >
> > > Hi all,
> > >
> > > Amber 12 PB routine doesn't work with FE atom-containing molecules. But
> > > Amber 11 works. I use .in-files created by MMPBSA.py in both versions:
> > the
> > > older one works, the output of 12th version contains a line
> > >
> > > PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE
> > >
> > > Best regards,
> > >
> > > Dmitry Mukha
> > > Institute of Bioorganic Chemistry,
> > > National Academy of Sciences of Belarus
> > > Kuprevich Street, 5/2, 220141, Minsk
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 14 2012 - 21:30:02 PST
