From: Sam Wallace (
Date: Thu Mar 26 2015 - 07:21:43 CDT

I'm wondering if anyone has attempted anything similar

What I'm trying to do is below

I have a psf and pdb of a molecule with a small linker joining two larger
I have performed some DFT calculations in a different program of the linker
only and have geometry output for a few states I'm interested in.
I would like to read in the output of the DFT calculations and then set the
geometry in the pdb file of just the linker component.
The approach I'm considering taking
The atoms of the linker in the PDB are conveniently id numbers 0 to 24. In
the DFT output the atoms aren't in the same order, but I could probably
build a map so they correspond correctly, thus any operation that reads
from an atom in the DFT output, could write to it's corresponding atom in
the PDB.
Where I'm a bit stuck for ideas is what operation to proceed with after
that point. I'm sure I could read the x, y, z coordinates from the DFT and
write them to the PDB, but that would result in the linker being displaced
from where it should be (to some degree)
Does anyone have any ideas on how to help?