From: gail louise dempsey <gd2f_at_cms.mail.virginia.edu>
Date: Fri 15 Sep 2000 12:25:34 -0400 (Eastern Daylight Time)

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

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.

Gail Dempsey
Received on Fri Sep 15 2000 - 09:25:34 PDT
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