[gmx-users] Problems with g_anaeig!

[Semen Esilevsky]

Ok, I've found the problem. It was my stupid mistake -
I forget that the filtered trajectory contains only CA
:) Thank you for help!

--- David van der Spoel <spoel at xray.bmc.uu.se> 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
> > 
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> 
> -- 
> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
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