Russell Green wrote:
Hello all,
I'm looking into performing dihedral PCA, but first I need to make an
appropiate index file. I would like to index the phi and psi angles for
a protein. I've searched in the archives but I didn't find anything
clear enough. I know I must specify four atoms for each, but could
someone kindly show me an example format?
try running mk_angndx
if you want to do it manually
you just need the atom numbers that make up the dihedrals.
(when you have this you need to run g_angle, then g_covar).
please look up earlier discussions on dihedral PCA on the list.
Thanks,
Russell Green
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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