[gmx-users] dihedral .ndx format

David van der Spoel spoel at xray.bmc.uu.se
Wed May 30 22:08:55 CEST 2007

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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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