AMBER: residue database

From: Lihua Wang <>
Date: Sat, 14 Aug 2004 17:55:59 -0400

Hi all,

I am little bit confused by the parameters in the residue database. Let's
say for parameters of dG (DG in

Atom N1 is of type NA and atom C8 is of type CK.

In parm99.dat, NA refers to "sp2 N in 5 memb. ring w/H atoms (HIS)", and
CK refers to "sp2 C 5 memb. ring in purines".

However, parm99.dat describes NC as "sp2 N in 6 memb. ring w/LP (ADE,GUA)"
and CQ as "sp2 C in 5 memb. ring of purines between 2 N".

Isn't NC a more appropriate type for N1 of DG and CQ for C8 of DG?
Since N1 is a sp2 N in 6 memb. ring. And CQ explicitly denotes sp2 C in 5
memb. ring of PURINES between 2 N

I would appreciate it if someone could kindly clarify this for me.


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Received on Mon Aug 16 2004 - 09:53:01 PDT
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