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