> 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.
No, this is not an issue here. I've made the same but without -ref option in both calls to g_covar, so no reference structure is needed. The result is the same: ------------- 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. ------------------------------------------------------- It seems to be a bug in g_anaeig or I severely misunderstood something! The filtered trajectory produced by g_anaeig have to be the same as original one, except the fact that only projections to specified principal components are kept, rigth? So, why the numbering of atoms in filtered trajectory appears to be different in such a way, that g_covar is happy with original trajectory, but not with the filtered one? Any other ideas how to test what's going on? Semen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] 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
