[gmx-users] Problems with g_anaeig!

Semen Esilevsky yesint4 at yahoo.com
Wed Jul 19 09:24:47 CEST 2006

> 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?


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