for PCA i used the g_covar followed by g_anaeig. i used the command line for g_covr as g_covar -f full.xtc -s full.tpr -o eig.xvg I have selected the protein for least square fit and main chain for covarience analysis. There is a warning message. WARNING: number of atoms in tpx (312) and trajectory (1061) do not match
The above command generates the files average.pdb, eigenvec.trr and eig.xvg Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig The commnan line for g_anaeig is given below. g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg For least square fit i have selected the protein and same for the eigenvectors This gave the following message; There were 40 inconsistent shifts. Check your topology where is the problem occured? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
