I have used antechamber (amber7) with gaff to produce a prep file with
bcc charges in a molecule that have a chain of alternate single and
double bonds. As the manual says, the default operation is to assign
both atom types and bond types, but in the simulation all of the C-C
bonds are trated alike, as I can see from the bond lengths evolution in
ptraj. Am I doing something wrong?
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Received on Wed Oct 22 2003 - 14:53:01 PDT
