VMD-L Mailing List

From: Aaron Larsen (alarsen_at_molbio.mgh.harvard.edu)
Date: Fri Jun 12 2015 - 08:03:25 CDT

Hello VMD users,

I'm in the middle of parameterizing a bunch of nucleobase like molecules
with the FFTK. Some of them are decorated with aminos. These amino groups
SHOULD be planar in geometry, reflecting the aromatic nature of the
heterocycles to which they are attached. However, FFTK seems intent on
treating these aminos as tetrahedral in geometry. It seems that there
should be a simple work around for this. Would anyone have any suggestions
on how to proceed?

It would be preferable if the solution did not involve starting over from
the Molefacture step.

Best,
Aaron