Re: Dihedral parameters for side-chains?

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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