Thank you for all your help! I think finding the analogous parameters has
worked!
-Julia
On Fri, Jul 8, 2011 at 3:26 PM, case <case.biomaps.rutgers.edu> wrote:
> 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 Tue Jul 12 2011 - 07:00:02 PDT
