Re: [AMBER] Regarding impropers from and guessing from bond topology

From: Daniel Roe <>
Date: Sat, 18 Oct 2014 17:24:23 -0600


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.


On Sat, Oct 18, 2014 at 3:38 PM, Arun Srikanth <> wrote:
> Hello amber users,
> I used 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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> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Oct 18 2014 - 16:30:02 PDT
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