From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Jul 06 2010 - 10:59:54 CDT
On Tuesday 06 July 2010 16:29:42 stefhoor wrote:
> how would one calculate the tilt between two helices along a
> simulation in namd. I would like to know if there are any analysis
> scripts written for it or tool or something like that.
> Thank you
It's not that hard if your simulation is aligned along a axis. Then you can
calculate the absolute tilt angle for both helices by their coordinates (for
example make a time series for the coordinates from the first and last amino
acid from each helix and "form a triangle with a axis of the coordinate
system") and from that the tilt angle between them.
If your system is not aligned to an axis, you have to wisely choose a
reference "axis" within your system, normalize your coordinates of the helices
to this reference and then you can calculate the relative tilt angle for each
and from that calculate the tilt angle between both helices.
The simples way would be to take one helix as reference, normalize the
coordinates to the reference and calculate the tilt angle for the second
helix. This would directly yield the tilt angle between the two helices.
I have done something similar with CHARMM so it should be way more easy if one
is familiar with TCL-Scripting within VMD.
And by the way, you might better ask you question on the VMD-Mailinglist since
most evaluation is done within VMD.
-- Bjoern Olausson Martin-Luther-Universitšt Halle-Wittenberg Fachbereich Biochemie/Biotechnologie Kurt-Mothes-Str. 3 06120 Halle/Saale Phone: +49-345-55-24942
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