Parameters for 5'-phosphorylated oligo-DNA

Alexei Botchkarev botchkar at fhs.csu.McMaster.CA
Wed Oct 9 11:02:23 EST 1996


Hi there

1. I have 5'-phosphorylated oligo-DNA in my structure and used
dna-rna.top and dna-rna.par in combination with
patch:
      FIRST  5PHO  TAIL + * END       {*5'-terminus with phosphate.*}
to generate it.

Check.inp execution was terminated with :

 %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
  bond energy constant missing. 
  target bond length missing. 
  ATOM1: SEGId="DNA1", RESId="11 ", NAME="O5T ", CHEMical="OH " 
  ATOM2: SEGId="DNA1", RESId="11 ", NAME="P ", CHEMical="P " 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODBON-ERR: program will be aborted. 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

(All run under 3.843).

Please, any ideas how to fix it easier. Is it better to make local patch
in the command file or to modify param file ?

 -------------

2. I wonder if anybody has expirience in combination of 

 TOPPAR:dna-rna-multi-endo.top  with
 TOPPAR:tophcsdx.pro

What kind of additional restraints (like arestraints.inp or 
brestraints.inp) in this case may be required ?



Alexey Bochkarev

Cancer Research Group
McMaster University 
Ontario
 





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