Dear Gromacs users!
There is some bug with g_anaeig the souce of which I could not fully understand. I have problems when I perform PCA of X-ray data set. Below you can my workflow. g_covar -f b2ar_xray_coors.pdb -s ref.pdb -o PCA_eigenval.xvg -v PCA_eigenvec.trr -av PCA_average.pdb -last 8 g_anaeig -v PCA_eigenvec.trr -s ref.pdb -f b2ar_xray_coors.pdb -rmsf eigrmsfPCA.xvg -filt here b2ar_xray_coors.pdb is the trajectory made from 10 X-ray structures of my protein (only main chain atoms are included) ref_pdb is the first frame of that trajectory As the result I've obtained reasonable eigenvalues and aigenvectors from g_covar BUT when I check filter trajectory ( produced by g_anaeig) fitted it to the ref.pdb or to the averaged structure in both cases I've obtained very distorted geometry of the protein in thefiltered trajectory. I have no such problems in case of PCA of MD trajectory ( when -f trajectory.trr is from the md snapshots not from x-ray structures) How it could be fixed ? James -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
