[gmx-users] add timestamp to frames

barrett barrett at biop.ox.ac.uk
Tue Jul 15 17:33:00 CEST 2003


how do you add timestamps to a set of pdbs in a trajectory saved from

I have a concatenated set of pdb files without any time stamps on the
I want to process them with g_covar. However g_covar dies immediately
complaining about too many iterations in jacobi.
I think this is because it is trying to read the timeframe and cannot
find it.

THEREFORE: I want to add timestamps to the frames of the trajectory.

I tried taking the individual frames as PDB files and then:

trjconv -f X.pdb -o X.xtc -t0 1
trjconv -f Y.pdb -o Y.xtc -t0 2

followed by

trjcat -o ensemble.xtc *aligned.xtc

but this failed:

Last frame          0 time    1.000
Fatal error:
Couldn't read time from second frame.

Suggestions very much appreciated


Dr Paul Barrett
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford

Tel 01865 275191
Fax 01865 275182

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