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
>
>
> _______________________________________________
> AMBER mailing list
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 28 2013 - 09:00:02 PDT
