[AMBER-Developers] Leap inconsistencies with wildcard torsion (surprise)

From: Niel Henriksen <shireham.gmail.com>
Date: Thu, 12 Nov 2015 17:19:14 -0800

Hi all,

I've noticed there have been many email threads over the years about wild
card torsions and what the proper behavior should be. Here is an example
<http://dev-archive.ambermd.org/200506/0024.html>. They mostly focus on
whether/how explicit torsion definitions should overwrite the wildcard
torsions. But I've stumbled on an odd case where Leap is inconsistent
within the same molecule. It's not mission critical at the moment, so this
is more a case study.

We have a small molecule, parameterized with GAFF, that has four
carboxylate groups attached to an sp3 carbon, like this: R-CH2-COO .

The problem occurs for the hc-c3-c -o torsion parameter, for which there
are sixteen instances in the molecule (four per carboxylate). In gaff.dat,
the following definitions exist:
X -c -c3-X 6 0.000 180.000 2.000 JCC, 7, (1986),
230
hc-c3-c -o 1 0.80 0.0 -1. Junmei et al,
1999
hc-c3-c -o 1 0.08 180.0 3. Junmei et al,
1999

I'm not 100% sure what is *supposed* to happen here, but I would think that
all instances of the torsion should be treated identically. Either all
sixteen instances of the torsion should get two terms (with periodicity 1
and 3), or they should all have three terms (with periodicity 1, 2, and 3).

Unfortunately, when I "printdihedrals" from the prmtop using parmed.py, I
find that ten of the instances get 2 terms, and six of the instance get 3
terms.

Fortunately the wildcard torsion has a barrier height of zero, so it
doesn't really matter in this specific case. But is it possible there
could be other instances like this lurking in GAFF where it does matter?

I've attached my prmtop/inpcrds for reference. And here are the parmed
commands to get the torsion info:
 printdihedrals .H23 @C37 @C38 @O10
 printdihedrals .H24 @C37 @C38 @O10
 printdihedrals .H23 @C37 @C38 @O32
 printdihedrals .H24 @C37 @C38 @O32
 printdihedrals .H31 @C43 @C44 @O12
 printdihedrals .H32 @C43 @C44 @O12
 printdihedrals .H31 @C43 @C44 @O25
 printdihedrals .H32 @C43 @C44 @O25
 printdihedrals .H27 @C40 @C41 @O11
 printdihedrals .H28 @C40 @C41 @O11
 printdihedrals .H27 @C40 @C41 @O26
 printdihedrals .H28 @C40 @C41 @O26
 printdihedrals .H19 @C34 @C35 @O9
 printdihedrals .H20 @C34 @C35 @O9
 printdihedrals .H19 @C34 @C35 @O24
 printdihedrals .H20 @C34 @C35 @O24

Thanks for your thoughts,
--Niel


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Received on Thu Nov 12 2015 - 17:30:03 PST
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