[gmx-users] Problems with g_anaeig!

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 19 09:26:21 CEST 2006

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
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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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