Hi Robert,
I too am continuing my education in the Amber file conventions so I'm eager
to read what others have to say. It would be helpful to know what the
system is, and what program you're applying. I just finished with a big
overhaul of the interpretations in impropers an other dihedrals in my own
program--the wildcards are tricky, but I'm taking X to mean wildcard at
face value.
My interpretation is that X matches anything and, because X cannot be
ordered alphabetically in improper dihedrals, X-X-CT-HC could then match
any improper dihedral with CT as the central atom and containing an HC as
one of the three other atoms. Can anyone comment on the validity of this
(and also speak to Robert's question, I don't mean to hijack his thread)?
Dave
On Wed, Apr 6, 2016 at 5:20 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> Good evening,
>
> I was hoping to clarify something from the Amber file formats page
> (http://ambermd.org/formats.html). Under improper dihedrals, there is a
> note written as follows:
>
> "Important note: all general type improper dihedrals (e.g. x -x -ct-hc)
> should appear before all specifics (ct-ct-ct-hc) in the parm list.
> Otherwise the generals will override the specific with no warning."
>
> I infer that this means that if one used the symbol "x" for the improper
> dihedral atom label (like IPT), it would encompass all atom types?
>
> I beg pardon if this is obvious, but trying to problem-solve why a
> system that should be planar does not remain so.
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
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Received on Wed Apr 06 2016 - 15:00:03 PDT
