On Mon, Dec 05, 2011, Urszula Uciechowska wrote:
>
> I have problems with proposing the atom types for the pyridine molecule ...
>
> Could not find angle parameter: CA - CA - NA
> Could not find angle parameter: CA - CA - NA
> Could not find angle parameter: CA - NA - CA
> Could not find angle parameter: HA - CA - NA
> Could not find angle parameter: HA - CA - NA
These are atom combinations that are not present in proteins or nucleic
acids, and hence not present in the standard Amber parameter files.
You can either use antechamber to assign GAFF atom types (and the
corresponding parameters), or you can assign parameters to the above
angles by analogy to similar parameters. To do this, you would use a text
editor to create a frcmod file with the appropriate missing parameters.
...good luck...dac
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Received on Mon Dec 05 2011 - 06:00:04 PST
