[AMBER] Regarding impropers from parmed.py and guessing from bond topology

From: Arun Srikanth <askforarun.gmail.com>
Date: Sat, 18 Oct 2014 17:38:36 -0400

Hello amber users,

I used parmed.py to get the impropers for my system. From the discussions
earlier I understood that the impropers are estimated from bond topology in
leap based on the definition

" an atom shared by three atoms and all three atoms lie on a plane".

However if I use some other tool to get the list of impropers for my
system. It differs from what leap assigns ?

Can you please explain why is this since both use the same definition of
impropers. Is it because the tolerance set in estimating whether the three
atoms are on a plane ?

AMBER mailing list
Received on Sat Oct 18 2014 - 15:00:03 PDT
Custom Search