Hi
I am trying to generate conformers by rotating user specified torsions on
rotatable bonds.
Initial idea was to generate Z-matrix , change torsion, convert to pdb,
apply forcefield and validate, but Z-matrix is inconsistent with bonding
pattern. I can't pinpoint bonds in Z-matrix.
Openbabel has obrotate which needs 4 atoms and angle to be specified and it
works but those atom numbers are taken from smiles/smarts which are not
according to the numbering in pdb taken from PDB/drugbank.
Openbabel also has function to get the number and position of rotatable
bonds/torsions.( to me it gave memory address and not the actual atoms,
bonds)
I find the modules in documentation of openbabel easier to understand but
little difficult to apply. Maybe after using babel some time I will be able
to understand the commands properly.
So my question is, is it possible to use openbabel to get the torsions and
rotate them(one at a time) according to use specified angle and write new
pdb/sdf to a file?
Thank You
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