On Tue, Jan 22, 2013 at 8:22 PM, James Starlight <jmsstarli...@gmail.com>wrote:
> Dear Gromacs users! > > > There is some bug with g_anaeig the souce of which I could not fully > understand. Good Advice: until you can almost write a code patch to fix it, be very hesitant in suggesting any software has a bug. The best people to help solve the issue are often those who wrote the code, and you don't want them annoyed with you :-) 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 ? > How have you excluded the hypotheses that your reference structure is not a valid representative of the middle of the range of variation? Or even that the X-ray structural ensemble really is one? Mark -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
