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help needed for generating hydrogen atoms in the synthetic ligand

Long Wang wang43 at purdue.edu
Thu Feb 3 12:30:09 EST 2005

I have  a  synthetic ligand in my structure, it is a  long unbranched
chain (CH2CH2CH2CONHCH2CH2CH2NHCOCH2CH2CH2). When I tried to run torsion
angle refinement in CNS 1.1, I got the following error messege.

 ERROR: There are no suitable base groups.
  This problem can be caused by isolated
  bonding networks with undefined or weak
  dihedral force constants.

The FAQ on CNS website suggested three ways to walk around this problem.
I like the last suggestion best, which is "include hydrogens for the
ligand molecule ". Although I had trouble to generate hydrogen atoms for
the ligand molecule. I wrote my topology and parameter file for the
ligand according to the parameters used for CH2E, C, O, N atoms in the
standard protein toppar file. I also ran the test case asking CNS to
generate hydrogen atoms in a small peptide using standard protein toppar
file.  It failed to generate hydrogen atoms connceted to CH2E atoms as
well. Anyone has successful experience or thoughts on this problem.


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