[gmx-users] dPCA "atoms"

Russell Green russellwgreen at gmail.com
Mon Jun 11 20:17:45 CEST 2007

Dear Gromacs community,

     I've been using the PCA analysis in dihedral space for a chain of my
protein of interest. I made a script to collect the atom quadruplets
corresponding to the phi and psi angles and output them to an index file. I
followed the steps in the paper manual and everything worked as it should;
however, is there any way to relate the dihedral PCA information to each
residue that contributed to the analysis? As it stands, my dummy reference
file contains 715 "atoms" but the analysis was done for about 536 residues
so that's 3 atoms per residue helping to define the dihedral angles. Could
someone please provide some suggestions or more insight? I've searched the
net and the mailing list but have found no information regarding my

Thanks in advance,
Russell Green
UAB Undergraduate Researcher
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