On Fri, Jul 08, 2011, Julia Blum wrote:
>
> Could not find bond parameter for: C - n3
> Could not find bond parameter for: c - N
> Checking for angle parameters.
> Could not find angle parameter: O2 - C - n3
> Could not find angle parameter: O2 - C - n3
> Could not find angle parameter: C - n3 - c3
> Could not find angle parameter: C - n3 - hn
> Could not find angle parameter: C - n3 - hn
> Could not find angle parameter: CT - C - n3
> Could not find angle parameter: h4 - c - N
> Could not find angle parameter: o - c - N
> Could not find angle parameter: c - N - H
> Could not find angle parameter: c - N - CT
> Could not find angle parameter: c3 - c - N
The other warnings look OK. Amber does not by default have any parameters for
covalent connections between GAFF atoms (lower case atom types) and Amber
atoms (Upper Case atom types.). You can either (a) make your SRP residue with
all Amber atom types, or (b) create a frcmod file with the above parameters,
probably just using analogous parameters from parm99.dat.
...dac
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Received on Fri Jul 08 2011 - 13:30:11 PDT
