[gmx-users] add timestamp to frames

[barrett]

Hi

Summary:
how do you add timestamps to a set of pdbs in a trajectory saved from
VMD.

Background:
I have a concatenated set of pdb files without any time stamps on the
frames.
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
etc..

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

Paul

Dr Paul Barrett
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
Oxford
OX1 3QU

Tel 01865 275191
Fax 01865 275182

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