AMBER Archive (2008)

Subject: AMBER: How to confirm atom types of small molecule perceived by antechamber

From: xiaonan zhang (
Date: Mon Jun 23 2008 - 03:39:30 CDT

Dear All
      I'm learning to use antechamber (AMBER 9) to simulate
protein-inhibitor complex. After reading the tutorial,
I managed to prepare topology and coordinate files for a complex.
     However, I am still nervous about the validity of the atom types and
bond order assigned to the inhibitor.
the prepin file have the atom types for every atom, but unfortunately I
cannot understand it because there
are no description about the naming conventions of these atom types in the

     Can anybody tell me where can I find the definition of these atom
types?? Or are there any other ways to
easily identify the bond orders or atom types?

Thank you!

Xiaonan Zhang
Shanghai public health clinical center

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