AMBER Archive (2003)

Subject: AMBER: Atom type in prepin file

From: Yong-Liang Zhu (yzhu_at_plexxikon.com)
Date: Wed Aug 13 2003 - 17:21:28 CDT

Hello all,

The parm99.dat file has the following atom types:

....
CA 12.01 0.360 sp2 C pure aromatic (benzene)
CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring
junction
CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS
CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C
CK 12.01 0.360 sp2 C 5 memb.ring in purines
CM 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6
......

However, in a prepin file generated by Antechamber from a purine like
compound, there were only CA (for all Cs in ring regardless in 5 or 6 member
ring in conjunction). So why there is no CB or CC while there supposed to
be?

Thank you.

Yong

******************************************
Yong Liang Zhu, Ph.D.
Senior Scientist, Bioinformatics
Plexxikon, Inc.
91 Bolivar Dr.
Berkeley, CA 98710
Tel: 510 647 4028
Fax: 510 548 4785
Email: yzhu_at_plexxikon.com
*************************************

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