AMBER Archive (2002)

Subject: RE: automated rescoring of ligands

From: Vickie Tsui (vickie_tsui_at_stromix.com)
Date: Tue May 14 2002 - 16:23:29 CDT

> We recognize that there are
> not (yet) very many examples of how antechamber fits in with the rest of
> the Amber package, and there are also a number of "rough edges" in this
> process, as you have found.

We've found some problems with Antechamber in terms of assigning types
for nitrile nitrogens - if anyone has experienced similar problems or
know of any fixes, please let us know. Otherwise Antechamber has been
a very useful tie between the small molecule world (esp. dealing with
many of them)and the protein/nuc. acid world in amber.