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
yong
-----Original Message-----
From: Sichun Yang [mailto:syang.physics.ucsd.edu]
Sent: Tuesday, April 08, 2003 8:45 PM
To: amber.heimdal.compchem.ucsf.edu
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.
Thanks,
Sichun
Received on Wed Apr 09 2003 - 02:53:01 PDT
