Dihedral parameters for side-chains?

From: Igor Petrik (petrikigor_at_gmail.com)
Date: Fri Apr 23 2010 - 11:50:30 CDT

Hi,

I am trying to develop parameters for an unnatural amino-acid
(chloroalanine). I wanted to compare some of the parameters to those of
natural amino acids cys and ser, however I can't seem to find the parameters
that would match any specific dihedrals around the CA (CT1)-CB (CT2) bond
for any sidechain in the parameter file (par_all27_prot_lipid.prm). The only
parameter that seems to match these dihedrals is X-CT1-CT2-X...

..
RESI CYS 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-*N*
ATOM CA CT1 0.07 ! *|* HB1
ATOM HA HB 0.09 ! *|* |
GROUP ! *HA-CA--CB--SG*
ATOM CB CT2 -0.11 ! *|* | \
ATOM HB1 HA 0.09 ! *|* HB2 HG1
ATOM HB2 HA 0.09 ! O=*C*
ATOM SG S -0.23 ! |
ATOM HG1 HS 0.16
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA SG CB N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 SG HG1
..

I guess my question/request is: can someone point out which specific
dihedral parameters NAMD/CHARMM uses to calculate torsional potentials
around CA-CB in Ser and Cys? That is to say, which parameters would be used
to calculate the energy of rotation around the CA-CB bond? I have spent
several hours and the wild card is the only parameter that I can come up
with that matches these dihedrals... :(

Thanks,
- Igor Petrik
University of Illinois, School of Chemical Sciences
Department of Chemistry
CLSL A325, Box 74-5
600 S Mathews
Urbana, IL 61801

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:55 CST