Re: [AMBER] tleap: C-N triple bond and sp1 hybridization

From: case <>
Date: Fri, 4 Jun 2010 12:49:34 -0400

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.


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Received on Fri Jun 04 2010 - 10:00:06 PDT
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