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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
      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

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

Alexey Bochkarev

Cancer Research Group
McMaster University 

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