VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Mon Aug 27 2007 - 03:30:41 CDT

Dear Johannes,

in the measure command the improper dihedral is defined exactly the same
way as the dihedral angle.
It is the angle between the planes defined by atoms {i j k} and by {j k
l}. Thus the angle depends on the order of atoms given in the measure
command. (However, the exacte reverse order of atoms yields the same
value.) This is the way impropers are defined in XPLOR and in the IMPR
statement of CHARMM topology files where the central atom is listed
first. Note that in the IC table of CHARMM topologies impropers are
listed in a different order: Here the central atom is the marked with an
asterisk (*), typically the second atom.

I hope this helps,
Jan

Johannes Müllegger schrieb:
> Dear VMD users/developers,
>
> I was wondering how the plan/vector angle is defined for the
> measure imprp function?
> If for example if the function is called like this:
>
> > measure imprp {i j k l}
>
> is the plane {i j k} and the vector {k l} i.e. the third atom central?
>
> Thanks,
>
> -hannes-
>
>
>
>
> Notice of Confidentiality: The information transmitted is intended
> only for the
> person or entity to which it is addressed and may contain confidential
> and/or
> privileged material. Any review, re-transmission, dissemination or
> other use of
> or taking of any action in reliance upon this information by persons
> or entities
> other than the intended recipient is prohibited. If you received this
> in error
> please contact the sender immediately by return electronic
> transmission and then
> immediately delete this transmission including all attachments without
> copying,
> distributing or disclosing the same.
>
>
> 

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de