AMBER Archive (2000)

Subject: C=C

From: gail louise dempsey (gd2f_at_cms.mail.virginia.edu)
Date: Fri Sep 15 2000 - 11:25:34 CDT

Dear Amber Community:

I am stuck on something, but first I want to thank Carlos
Simmerling, Frank Yan, Peter Gannett, Samantha Hughes,
Piotr Cieplak, and Bill Ross for your wonderful
suggestions. I haven't tried MOIL-View or VMD yet, because
I have not had a successful run on AMBER yet.

I am trying to build a molecule that has conjugated double
bonds that are not in ring formation. Which atom type
should I use for the sp2 carbons (-C=-C=C-)? Currently I
get errors when I try to "saveamberparm x xbox.top
xbox.crd".

Cannot find bond parameter for C-C
Cannot find bond parameter for C-HC
....
Cannot find angle parameter for 0-C-O2
...and the list goes on.

Any suggestions would be greatly appreciated.

Sincerely,
Gail Dempsey