Hi,
Without more details on how this different tool you are using defines
impropers, and perhaps a simple of example of how its output differs
from leap, I don't think we will be able to answer your question.
-Dan
On Sat, Oct 18, 2014 at 3:38 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> 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 ?
>
> Thanks
> Arun
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Sat Oct 18 2014 - 16:30:02 PDT
