From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Tue Jul 06 2010 - 11:48:22 CDT
> 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.
You are possibly posting to the wrong list. Having said that, calculating
crossing angles for associating helices is not as straightforward as you
may think. You would normally have to calculate the local helix axis for
each helix, and then work your way from there. Once upon a time, there was
a program called HELANAL (written in FORTRAN77(?), that's why I am using
capital letters) which could do the trick (and much more). I bet there are
more recent and automated programs available these days, but a quick
search showed that HELANAL is still available. Needless to say that you
probably can't do the calculation directly with your DCD file (save PDB
files from the DCD and work with them).
Nicholas
--
Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
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