AMBER Archive (2009)

Subject: Re: [AMBER] OE and CG types

From: Dean Cuebas (deancuebas_at_missouristate.edu)
Date: Sat Dec 26 2009 - 19:10:06 CST

> I think you're still confused - there is no CG atom type in Glu, it's an
> atom named CG. names and atom types are different.
> here are the GLU names (column 1) and atom types (column 2) for each atom -
> this is from dat/leap/prep/all_amino94.in in case you want to know more.
>
> N N
> H H
> CA CT
> HA H1
> CB CT
> HB2 HC
> HB3 HC
> CG CT
> HG2 HC
> HG3 HC
> CD C
> OE1 O
> NE2 N
> HE21 H
> HE22 H
> C C
> O O

The atom names on the left correspond to the convention of Greek alphabet,
with alpha being "next to" the highest priority functional group, the C=O,
whose carbon is simply labeled C and whose oxygen is named O.

Beta, "next to that"...etc.

CA = the C alpha carbon
CB= the C beta carbon
CG= the C gamma carbon
CD = the C delta carbon
OE= the O in the epsilon position

etc...

Do not confuse those with the atom types...

BTW, you have GLN up there, not GLU...

Good luck...

Dean 

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas_at_missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

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