VMD-L Mailing List

From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Thu Jun 09 2011 - 11:40:57 CDT

Hi

We suggest these tutorials. These help you to make topology file and force field
file.

===> to create topology file:
Topology File Tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/
===> to create force field file:
Parameterizing a Novel Residue:
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/

Hope this helps you
Sajad and Zahra

________________________________
From: "Bennion, Brian" <Bennion1_at_llnl.gov>
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Sent: Thu, June 9, 2011 1:44:31 AM
Subject: vmd-l: parameterization tool

Hello All,

I have run into some issues with the vmd1.9 based paramtools extension.
First, when loading a frequency job i get an error stating that hesstrans is an
invalid command.

Second, after all files are loaded or the project file is finally loaded, I
select the edit->atom properties

A new window is displayed with the atoms and the known properties. However, in
the editable atom properties window where one adds or modifies atom information
like charges and names, it appears that the VDWrmin14 field has been populated
with the default 0.000 charges and the lewis fied now contains the NPA atomic
charge.

This is very annoying in that you must change the value in the lewis field back
to an integer value if you want to submit any other changes that you made to
that atoms properties.

Does anyone else use this extension?

Sincerely
Brian Bennion