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patching a residue

Charlie Bond charlieb at biochem.usyd.edu.au
Sat May 24 01:12:38 EST 1997


chris dealwis wrote:
> 
> I am trying to patch a lysine residue to a cofactor with the following
> toplogy and parameter statements.

>  ADD BOND 2C4A 1NZ
>  ADD ANGLE 1CE 1NZ 2C4A
> {}
>  DIHE 1CE  1NZ 2C4A 2C4
> 
> IMPR 2C4 2C4A 1NZ 1CE
> END {PPLP}
> 
> the parameter file entry is:
>  BOND 2C4A 1NZ    3020.0  1.500 !
> 
> When I try to do posistional refinement I get the following error
> message
> 
>  %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
>   bond energy constant missing.
>   target bond length missing.
>   ATOM1: SEGId="P   ",  RESId="1   ",  NAME="C4A ",  CHEMical="CX13"
>   ATOM2: SEGId="B   ",  RESId="87  ",  NAME="NZ  ",  CHEMical="NH3 "
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>  %CODBON-ERR: program will be aborted.
> 

I think that your BOND statement should use the atom types CX13 and NH3
rather than their names C4A and NZ

Cheers,
Charlie

PS: Your email reply address is set incorrectly.



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