VMD-L Mailing List

From: Elena Lilkova (elilkova_at_phys.uni-sofia.bg)
Date: Tue Jan 06 2015 - 07:32:57 CST

Dear VMD community,

I want to parameterize a novel molecule with FFTK. So, I decided to repeat
the example from the screencasts. I am currently at the Bond and Angle
Parameters Optimization step. I noticed that the angle force constants
that I obtain are significantly different from the ones displayed in the
screencast. They are at least an order of magnitude, sometimes even two
orders, larger than what you show. I even tried to start with values,
similar to the those from the screencast and then optimize, but once again
I ended up with force constants in the range 40. - 350.
I am new to novel molecules parameterization, but these force constants
seem quite large to me. I followed strictly the procedure from the
screencasts and I don't know why I obtain such different results. Any
ideas/explanations/comments?
I am using VMD 1.9.2a42. The QM simulations were done with Gaussian 09.

Elena Lilkova

elilkova_at_phys.uni-sofia.bg

PhD student,
Atomic Physics Department,
Faculty of Physics,
University of Sofia "St. Kliment Ohridski"

5 James Bourchier Blvd.
1164 Sofia,
Bulgaria