Hi,
Without seeing your cpptraj input and output I can only guess, but I
think you are trying to do a surface area calculation right? This
error is happening because the code doesn't have surface area
parameters for Na+, so it is defaulting to "N" (nitrogen) and stating
that 0 bonds to N is unusual. If you are calculating surface area and
you don't care about the ions (not sure why you would) you can just
strip them out before you do the calculation, e.g.:
parm prmtop
trajin trajectory.nc
strip :Na+,Cl-
surf out surf.dat
Let me know if this helps. If not, please attach your cpptraj input
and output and we'll figure this out.
-Dan
On Wed, Jun 1, 2011 at 1:01 AM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber developers,
>
>
>
> Thank you for usual support.
>
>
>
> I would like to ask an error message below, which I encountered in running
> cpptraj module in AmberTools 1.5.
>
>
>
> Warning: Unusual number of bonds for atom 4725 (0), type Na.
>
>
>
>
>
> This statement could appear in what situation?
>
>
>
> I used a prmtop file consists of 2 Protein chains, 4 Cl- and 1 Na+.
>
> The ptraj can be worked with the same prmtop file but Cpptraj was not.
>
>
>
> Some cpptraj commands can be useful for my study and
>
> I really use the cpptraj.
>
>
>
> Thank you for kind support.
>
>
>
> Ikuo Kurisaki
>
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>
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Received on Wed Jun 01 2011 - 04:30:02 PDT
