From: Jun Zhang (coolrainbow_at_yahoo.cn)
Date: Sat Apr 24 2010 - 22:29:12 CDT
Hi Igor :
There is one line(2139) in the file:
X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
Do you think it is what you need?
Jun Zhang
Nankai University
coolrainbow_at_yahoo.cn
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
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