Dear Jason,
Thank you very much for your help. It works fine with setting inp=1 and radiopt=0 in the &pb.
However, it's not clear to me. Why do we have to set these two parameters, since inp=1 and radiopt=0 are default? They should not set explicitly.
Best Regards,
Xioling
> Date: Thu, 28 Mar 2013 11:37:30 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI
>
> This type of error has been discussed before. For instance here:
> http://archive.ambermd.org/201208/0072.html
>
> setting inp=1 and radiopt=0 in the &pb section will use a simple surface
> area-dependent term (similar to GBSA) to calculate the non-polar solvation
> free energy (and radiopt=0 will instruct pbsa to use the radii from the
> prmtop file).
>
> HTH,
> Jason
>
> On Thu, Mar 28, 2013 at 11:25 AM, Xioling Chuang <xioling_c.hotmail.com>wrote:
>
> > Dear All,
> >
> > I am using mmpbsa calculation in amber12 to calculate decompose energy.
> > The input is is
> >
> > -------
> > title
> > &general
> > startframe=1, endframe=20,
> > interval=1, keep_files=1,
> > verbose=1,
> > /
> > &gb
> > igb=2, saltcon=0.0,
> > /
> > &pb
> > istrng=0.0,
> > /
> > &nmode
> > nmode_igb=1, nmode_istrng=0.0,
> > drms=0.1, maxcyc=1000,
> > /
> > ---------
> >
> > I got the error,
> >
> > PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI
> >
> > I use parm10.dat. Since the system is DNA in which the atom type "CI" was
> > assigned for atom C5', there should not have any problem with parameter.
> > What is wrong in my case?
> >
> > Thank you very much,
> > Xioling
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Mar 28 2013 - 09:00:03 PDT
