From: Martin, Erik W (
Date: Thu Mar 26 2015 - 12:53:29 CDT

Maybe this will or won't solve your problem. However, I have done (what I think) are similar things before. I have always had a long linker I've needed to model though...

Anyway, why not use this workflow:

1. write a pdb of your dft optimized geometry

2. using several atoms from the linker align one subunit with the appropriate end of your dft structure

3. repeat with the other subunit

4. write pdbs containing non-overlapping molecules

5. merge pdbs

6. write new psf


From: <> on behalf of Sam Wallace <>
Sent: Thursday, March 26, 2015 7:21 AM
Subject: vmd-l: Script to impose coordinates from separate file onto equivalent selection of atoms

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 substituents.
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--_000_142739240893477259STJUDEORG_--