Dear Priti,
> Could not find bond parameter for: C - sh
> Could not find bond parameter for: o - N
> Building angle parameters.
> Could not find angle parameter: O - C - sh
> Could not find angle parameter: C - sh - hs
> Could not find angle parameter: C - sh - c3
> Could not find angle parameter: CT - C - sh
> Could not find angle parameter: o - N - H
> Could not find angle parameter: o - N - CT
> Could not find angle parameter: c1 - o - N
> Building proper torsion parameters.
> ** No torsion terms for O-C-sh-hs
> ** No torsion terms for O-C-sh-c3
> ** No torsion terms for CT-C-sh-hs
> ** No torsion terms for CT-C-sh-c3
> ** No torsion terms for c1-o-N-H
> ** No torsion terms for c1-o-N-CT
> ** No torsion terms for c3-c1-o-N
Building parameters from scratch is hard work and requires a lot of fitting
to quantum and experimental data. As a first approximation however, for the
missing GAFF to FFXX parameters I would obtain the GAFF force field paper
and then see if you can find similar parameters.
E.g. for
C-sh
I would look at what Gaff would give for the following system:
O
||
CH3-C-S-H
Then add that to an frcmod file as the type C-sh.
If the parameters are missing from the GAFF force field you could always
build a suitable 'model' compound of the connection region and run it
through antechamber to see if it will interpolate parameters for you.
This will be a reasonable guess at the parameters that you can always tweak
later.
I hope this helps.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sat Jan 14 2006 - 06:10:07 PST
