On Mon, Sep 12, 2011, Darren Jindal wrote:
> I have a question regarding the implementation of nonstandard residues in
> AMBER.
>
> Building bond parameters
>
> Could not find bond parameter for : C - NT
>
> Building angle parameters.
>
> Could not find angle parameters: O - C - NT
Amber (antechamber) doesn't have any automatic way of getting all needed
parameters for the Amber force field itself, just for gaff. Hence, you will
need to make your own frcmod file containing the parameters you need. Often
you can do this be analogy to parameters that already are present. Or, you
could build the residue with gaff, look at the parameters it uses, and copy
those over to the corresponding ones for the Amber potentials. But some
thinking and hand-editing are required.
...good luck...dac
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Received on Tue Sep 13 2011 - 05:00:03 PDT
