VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Jun 12 2015 - 10:18:00 CDT

Aaron,

I'm not sure what you mean by:
> FFTK seems intent on treating these aminos as tetrahedral in geometry

Can you expand on where the perceived problems with geometry are occurring?

Regards,
Christopher Mayne

On Jun 12, 2015, at 8:03 AM, Aaron Larsen wrote:

> 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