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

From: case <>
Date: Fri, 4 Jun 2010 08:43:38 -0400

On Fri, Jun 04, 2010, vedat durmaz wrote:

> i'm trying to use an acetonitrile residue (prep/frcmod/pdb, downloaded
> from the manchester site, modified a little) in tleap in order to
> produce .inpcrd/.prmtop files and simulate a system with acetonitrile as
> solvent.
> when i add two new atom types as follows in tleap with sp1 hybridization
> (C-N) and load my pdb file i get an error message. (in contrast, it
> works well with atom types sp2-sp2).
> > addAtomTypes { { "YC" "C" "sp1" } { "YN" "N" "sp1" } }
> > C3N=loadpdb ch3cn.pdb
> Loading PDB file: ./ch3cn.pdb
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported

Don't worry about that is misleading.

> +---Tried to superimpose torsions for: *-C3-C2-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved

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.

That said, none of what you posted is an error -- everything may be OK.


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Received on Fri Jun 04 2010 - 06:00:26 PDT
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