Closed michelsanner closed 4 years ago
Apologies. I should have dug a little more before asking
I realize now Modeller provides support for this modeller = Modeller(fixer2.topology, fixer2.positions) modeller.add(fixer1.topology, fixer1.positions)
did the trick -M
Glad you figured it out!
Hello I am wondering is there is an easy way to "combine" 2 fixed moelcules. Basically I am creating a fixer for a first PDB file
fixer1 = PDBFixer(filename=pdb1) fixer1.findMissingResidues() fixer1.findMissingAtoms() fixer1.findNonstandardResidues() fixer1.addMissingAtoms() fixer1.addMissingHydrogens(7.4) fixer1.removeHeterogens(False)
then create fixer2 for the second molecule and I would like to write you the PDB (or prmtop, and coordinate file) for the complex of the 2
It seems that fixer2.positions.extend(fixer1.positions) does what I expect. I tried for n, chain in enumerate(fixer1.topology.chains()): chain.id = n+1 chain.index = n+1 fixer2.topology.addChain(chain)
but when I writ to write out the PDB for the complex I get ValueError: The number of positions must match the number of atoms
Would it be reasonable/possible to add an add operator to PDBfixer to perform this ?
thanks for any advise
-M