Dear Open Babel users,
I'm writing a script to reconstruct a complex of two peptides. I employ OB python interface and also Pybel to make necessary transformations of both peptides, but finally I have to perform energy minimization of the whole complex to avoid bumping of side chains.
It seems to be possible, since when I load two molecules from one PDB file, OB can optimize them. But here I don't know how to combine two molecules into one object that I could apply energy-minimization routine for the system.
Can you help, please?
It seems to be possible, since when I load two molecules from one PDB file, OB can optimize them. But here I don't know how to combine two molecules into one object that I could apply energy-minimization routine for the system.
Can you help, please?
PS. Let's say, molecules are defined as the following:
H1 = pybel.readfile('pdb', 'pep1.pdb').next()
H2 = pybel.readfile('pdb', 'pep2.pdb').next()
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