Subject: RE: ArgusLab 4 question

From: "Mark Thompson" <mark/at/arguslab.com>
Date: Thu, 30 Oct 2003 08:23:34 -0800

Richard,

Would you send me the structure file for your peptide?  The error is almost
certainly that the am1.prm file does not contain zinc parameters (though I'm
sorry you received a cryptic exception message, and I'll look into cleaning
that up).  Also, ArgusLab4 is currently a beta1 release and still contains
little (and big) irritations.

Regarding a higher-level of theory, you have a couple of options.

1. You can try PM3 in ArgusLab; which does support Zn.
2. If you have Gaussian98 or Gaussian03 available, you can run it directly
> from ArgusLab's Gaussian interface.
3. You can have ArgusLab save the Gaussian input file and you can run it on
another machine.
4. You can save the molecule as an xyz, pdb, or mol file which can be read
by a number of other academic and commercial packages.

Please let me know if I can be of more help.

Also, you might consider joining the ArgusLab user's group.  It's another
good place to find out about bug fixes, and solutions to issues that others
have found. (Go to http://www.arguslab.com  and click on "Users Group"
button).

If you have any other feedback, I'd like to hear about it.  Feel free to
send me email.  The peptide builder is new and I'd be interested in hearing
if you liked it or had any suggestions.

Best regards,
Mark Thompson

***************************
Mark Thompson, PhD
Planaria Software LLC
PO Box 55207
Seattle, WA  98155

mark/at/arguslab.com
http://www.arguslab.com
***************************

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request/at/ccl.net]On
Behalf Of Richard Wood
Sent: Wednesday, October 29, 2003 2:34 PM
To: chemistry/at/ccl.net
Subject: CCL:ArgusLab 4 question

Hi all

I have a molecule that I've built in ArgusLab4.  It's a small peptide
that has a Zinc in it.  I have optimized it using the Universal Force
Field (UFF).  Is there a way that I can "convert" my file so that I can
do an optimization using a higher level of theory?  For example, if I
try to do an AMI calculation, I get an error message saying,
"Unrecognized exception caught in  runCalcThread".

Thanks in advance,
Richard