On Fri, Jun 04, 2010, vedat durmaz wrote:
> You should check the atom types for atoms C2 and C3 (use the "desc"
> command in > tleap). The reference to "sp0" usually means a missing
> atom type.
>
> desc C3N
type this: "desc C3N.1" which will show you the atom types of each atom.
>
> i'm confused after having saved a lib file with
>
> saveoff C3N ch3cn.lib
>
> its "!entry.C3N.unit.connectivity" section only shows ONE line (single
> bond) for N1-C2. in contrast, having used
>
> addAtomTypes { { "YC" "C" "sp2" } { "YN" "N" "sp2" } }
>
> instead, results in 2 lines (=double bond) for N1-C2 in the
> "!entry.C3N.unit.connectivity" section of the lib file.
This is not correct. Connectivity should only be reported once -- amber
doesn't really use bond orders for anything, so a bond between two atoms
should not get repeated two or three times for double or triple bonds.
It's often easer to look at the mol2 file, if that helps.
....dac
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Received on Fri Jun 04 2010 - 10:00:06 PDT
