I have another question about g_anaeig: If I use -proj option in conjuction with -first and -last the program writes projection of only one first eigenvector. As I understand it should be one column for each eigenvector in the range. What's wrong?
--- David van der Spoel <[EMAIL PROTECTED]> wrote: > Semen Esilevsky wrote: > >>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. > > > ------------------------------------------------------- > > how many atoms in your traj and your tpr? > > programs may read a (default) tpr file without you > explicitly passing > the tpr file. > > > > > > > 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 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 > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > 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 > __________________________________________________ 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
