RE: Trying to understand parm99.dat

From: Yong Duan <>
Date: Tue, 8 Apr 2003 21:48:48 -0400

Dear Sichun,

AMBER uses "atom types" to identify the dihedrals, not atom names.
Decoupling atom types from atom names is a standard practice and allows
quite a bit of flexibility.

The dihedral that you were asking, N-CA-C-N, is one of the main-chain
dihedrals of peptides.
This is identified as N-CT-C-N in parmxx.dat

-----Original Message-----
From: Sichun Yang []
Sent: Tuesday, April 08, 2003 8:45 PM
Subject: Trying to understand parm99.dat

Dear All,

I am trying to understand how parm99.dat works.
For example, I have a dihedral N -CA-C -N. Then how does it call from
the file parm99.dat? To be specific, which line(s) in parm99.dat can be
applied to this dihedral N -CA-C -N? I only find X -C -CA-X can be used
for that, but it seems that it is not enough. I hope I have made my
question clear. Thank you for your explanation.

Received on Wed Apr 09 2003 - 02:53:01 PDT
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