Francois, please try the JAR files in
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
These have a new mol2 reader that recognizes AMBER and GAFF atom types.
Needs checking.
Bob
On Thu, Oct 30, 2008 at 6:44 AM, FyD <[EMAIL PROTECTED]> wrote:
> Dear Angel,
>
> > In your DMSO file, the atom type for the offending atoms is CT and H1.
>
> Yes, I agree.
>
> > This is not supported by mol2 spec. See
> > http://www.tripos.com/mol2/atom_types.html
> > http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html
>
> Yes
>
> > If you cahnge that to just C and H, Jmol behaves. You should maybe
> > use the proper types, which seem to be C.3, H, S.o, O.2
> > They also work in Jmol.
>
> OK, but you consider here only the force field atom types from the
> Tripos force field. This means Jmol is not compatible with other force
> fields such as CHARMM, AMBER, etc... I think it would be more suitable
> that Jmol understand many force fields and not only this Tripos force
> field. The Tripos file format can be used by many programs different
> from Tripos Inc.
>
> For instance Amber force fields use CT, H1 force field atom types.
> This is why I provided CT, H1 in the force field atom type column of
> the DMSO.mol2 file...
>
> regards, Francois
>
>
>
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--
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