hi, On Tuesday 18 July 2006 12:12, Semen Esilevsky wrote: > Dear gmx users, > I've found a strange problem in g_anaeig. > I'm trying to project the trajectory into few first > eigenvectors. For this I first do: > > g_covar -f md_all.xtc -s md0.tpr -n index.ndx -fit > -ref -pbc -tu ns > > Chosing CA group for matrix construction. > Then I pick the resulting file eigenvec.trr and do: > > g_anaeig -v eigenvec.trr -f md_all.xtc -s md0.tpr > -filt -n index.ndx -first 1 -last 10 > > Everything works fine and the output file filtered.xtc > should contain nice filtered trajectory. Ok, let's > test: > > g_covar -f filtered.xtc -s md0.tpr -n index.ndx -fit > -ref -pbc -tu ns > ... > ... > ... > Calculating the average structure ... > Reading frame 0 time 0.000 > ------------------------------------------------------- > Program g_covar, VERSION 3.3.1 > Source code file: mshift.c, line: 118 > > Fatal error: > Molecule in topology has atom numbers below and above > natoms (238). > You are probably trying to use a trajectory which does > not match the first 238 atoms of the run input file. > You can make a matching run input file with tpbconv. > ------------------------------------------------------- > > What is wrong? It should be the same trajectory as > initial md_all.xtc but with different numbers. > Any ideas?
You have to use also a reference file with the same amount of atoms in it, like your new trajectory. Use something like trjconv or as the error msg say tpbconv to write out a gro/pdb file only with CA atoms. > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
