I would suggest following the antechamber tutorial:
TUTORIAL B4: Simulating a pharmaceutical compound using antechamber
and the Generalized Amber Force Field.
That should clear up how to do what you need to do, although whether
or not the parameters are valid is for you to check on your own.
On Sep 21, 2008, at 9:34 AM, babak minoofar wrote:
> Dear amber users,
> I am trying to use tleap to make toplogy file for
> bis(trifluoromethylsulfonyl)imide (Tf2N) but there are some missing
> parameters and tleap complains that cannot make toplogy file. Is
> anybody can help
> to find missing parameters.
>
> the message from leap:
> Building angle parameters.
> Could not find angle parameter: s6 - c3 - f
> Could not find angle parameter: s6 - c3 - f
> Could not find angle parameter: s6 - c3 - f
> Could not find angle parameter: ne - s6 - o
> Could not find angle parameter: ne - s6 - o
> Could not find angle parameter: ne - s6 - c3
> Could not find angle parameter: o - s6 - ne
> Could not find angle parameter: o - s6 - ne
> Could not find angle parameter: s6 - ne - s6
> Could not find angle parameter: f - c3 -
> s6
> Could not find angle parameter: f - c3 - s6
> Could not find angle parameter: c3 - s6 - ne
> Could not find angle parameter: f - c3 - s6
> Could not find angle parameter: s6 - c3 - f
> Could not find angle parameter: s6 - c3 - f
> Could not find angle parameter: s6 - c3 - f
> Could not find angle parameter: ne - s6 - o
> Could not find angle parameter: ne - s6 - o
> Could not find angle parameter: ne - s6 - c3
> Could not find angle parameter: o - s6 - ne
> Could not find angle parameter: o - s6 - ne
> Could not find angle parameter: s6 - ne - s6
> Could not find angle parameter: f - c3 - s6
> Could not find angle parameter: f - c3 - s6
> Could not find angle parameter: c3 - s6 - ne
> Could not find angle parameter: f - c3 - s6
> Building proper torsion parameters.
> ** No torsion terms for o-s6-ne-s6
> ** No torsion terms for o-s6-ne-s6
> ** No torsion terms for s6-ne-s6-o
> ** No torsion terms for s6-ne-s6-o
> ** No
> torsion terms for s6-ne-s6-c3
> ** No torsion terms for c3-s6-ne-s6
> ** No torsion terms for o-s6-ne-s6
> ** No torsion terms for o-s6-ne-s6
> ** No torsion terms for s6-ne-s6-o
> ** No torsion terms for s6-ne-s6-o
> ** No torsion terms for s6-ne-s6-c3
> ** No torsion terms for c3-s6-ne-s6
> Building improper torsion parameters.
> total 0 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
> Quit
>
>
>
> Regards
> Babak
>
>
>
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Received on Mon Sep 22 2008 - 05:07:33 PDT
