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
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
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Received on Wed Nov 14 2012 - 10:30:03 PST
