On Mon, 2014-03-31 at 15:45 +0100, Hannes Loeffler wrote:
> Hi,
>
> as far as I am aware of the central atom in an improper is always the
> third atom. I think in the attached example (cyclopropyl-benzene) the
> order is wrong for C5-H-C-C1. In the parmtop the order of indices is
> 18(H) 0(C) -15(C5) -3(C1). Shouldn't that be -0 in third position?
You've hit probably the one case that the topology file is entirely
unprepared to handle. All of the topology file writers (tleap, cpptraj,
and ParmEd) will automatically reverse any dihedral in which the first
atom is in the 3rd or 4th position.
The reason is that -0 == 0, so with the first atom in either the 3rd or
4th position there is no way to determine whether or not the term is an
improper or if end-group interactions should be ignored.
The upside here is that Amber treats all impropers the same as it treats
proper torsions, so the energy will be identical compared to listing it
as 3, 15, -0, -18. So this may pose problems in some corner cases
(mainly if you're trying to manipulate the topology file with ParmEd),
but will not affect sander or pmemd at all.
Thanks for the report,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 31 2014 - 09:00:03 PDT
