As I understand that primarily the connections between atoms is
established by analysis (by prep program) of tree (e.g. letters
M,B,3,E,...) not by those connectivity numbers. You can test it by
putting any numbers in those places. Hope leap is doing the same job.
Piotr
On Fri, 2008-03-14 at 09:11, Ross Walker wrote:
> Hi All,
>
> I'm not sure if we still ever use the prep files in
> $AMBERHOME/dat/leap/prep/ however, there appears to be a typo in
> all_nuc94.in. The bond connectivity for DC3 appears to be wrong.
>
> The last line:
> 34 H3T HO M 30 25 8 0.96 114.97 180.00 0.4396
> Should probably be:
> 34 H3T HO M 33 25 8 0.96 114.97 180.00 0.4396
>
> It does not look like this typo affects all_nucleic94.lib so is likely
> benign. However, I am wondering if anyone knows more about the prep files
> and whether this really is benign (or even an error in the first place).
> Should we update it in AMBER 9 and presumably AMBER 10?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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Received on Sun Mar 16 2008 - 06:07:42 PDT
