VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Apr 10 2013 - 11:56:31 CDT

As stated elsewhere on this list, paratools should not be used any more. ffTK is the route to go.
Obviously you still run into the same problem since ffTK is tied to Gaussian output.
Perhaps you could seek out a collaboration?
Or maybe build one unit of the chain by hand using the already published forcefields and parameters from the literature. It is indeed a simple molecule

Brian

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of kerexen_at_gmail.com
Sent: Wednesday, April 10, 2013 8:41 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: parameters for PE100 chain?

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