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 <fyd@q4md-forcefieldtools.org> wrote:
Dear Angel,

> In your DMSO file, the atom type for the offending atoms is CT and H1.

Yes, I agree.
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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Robert M. Hanson
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If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900