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
