From: Mayne, Christopher G (
Date: Wed Apr 10 2013 - 12:36:23 CDT

If "PE1000 chain" is polyethylene glycol, the breathe easy--the parameters exist. See top_all35_ethers.rtf in the CHARMM36 release.

For future reference, ParaTool has been depreciated in favor of the Force Field Toolkit (ffTK).

Christopher Mayne

On Apr 10, 2013, at 10:41 AM, <>

> Hello,
> I am to setup a model environment for a PE100 chain in water. I have the
> pure PDB file for coordinates, and I am doing this setup for study, with no
> experience. I have done the topology part successfully with TopoTools.
> Now I feel stuck at the point of ParaTool "File->Setup QM geometry
> optimization" with two dead-ends, either waiting for the next release of VMD
> with GAMESS support, or pay ~$6000 for Gaussian (not an option).
> Please help me making the parametrization for NAMD modelling.
> Regards,
> Tibor Venyige