On Tue, Apr 21, 2015, Sanja Zivanovic wrote:
>
> after using antechamber and parmchk I could not obtain parameters and got
> error for some angles and dihedrals:
>
> CA-N3-C -O 1 0.000 0.000 0.000 ATTN, need
> revision
> CA-N3-C -N3 1 0.000 0.000 0.000 ATTN, need
> revision
> N3-C -N3-H 1 0.000 0.000 0.000 ATTN, need
> revision
> N3-C -N3-CR 1 0.000 0.000 0.000 ATTN, need
> revision
> H -N3-C -O 1 0.000 0.000 0.000 ATTN, need
> revision
>
> Could you please advise me how can I fix this?
To get started, you can try to find analogous parameters elsewhere. (N3
is probably very close to NT.) Or, use gaff atom types rather than Amber
types, since they cover a much wider range of chemical environments. If
you really need Amber atom types, run antechamber with gaff types anyway,
and copy analogous parameters to the Amber types frcmod file.
Above is all just to get started. Depending on what you are trying to do, you
made need to use a much more elaborate procedure, based on quantum mechanical
calculations. See the mdgx or paramfit chapters in the Amber Manual.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 22 2015 - 08:30:02 PDT
