Hi, I want to perform the dihedral PCA for two residues of a turn region in a protein i.e 4 dihedral angles. I have created an index file for the atoms constituting phi and psi angles for those two residues. But I don't understand what has to be written in covar file .. According to manual it says "covar.ndx, which necessarily contains one group of atom 1 to integer(2*N/3), where N is the number of dihedral angles". I don't get the meaning of this line ?? Can anybody guide me ...
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