From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Thu Jun 09 2011 - 11:52:29 CDT

Hello
Thank you for your suggestion. However, these suggestions have nothing to do with the questions that I asked below.
Please note that the behavior I report below would happen regardless of whether I followed the tutorials or not.

The first problem has been fixed and is checked into the vmd CVS. The hesstrans command should have been hessiantransform in the tcl plugin code.
The second issue is caused by reading in save project files. The read/write logic is faulty and currently under examination by the developers.

In synopsis, 1 bug is fixed in the source code, the second only occurs if a previously saved project file is loaded.

Best regards
Brian Bennion

-----Original Message-----
From: sajad falsafi [mailto:sajad.falsafi_at_yahoo.com]
Sent: Thursday, June 09, 2011 9:41 AM
To: Bennion, Brian; vmd-l ks.uiuc.edu
Subject: Re: vmd-l: parameterization tool

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