[gmx-users] g_RMS: Mismatch of atom number between topology and reference structure

Sergio Manzetti sergio.manzetti at vestforsk.no
Mon Mar 7 09:33:31 CET 2011

Hello, I am doing a refolding experiment, but I re-experience the same
error. First of all, I use pdb2gmx for an input PDB structure, choose
OPLS/AA force field and vacuum settings (no waters).

Then I amke a box, and start simulations.

What I want to do is to compare the starting unfolded structure of the
simulation and its changes during the sim (all represented as a traj.xtc) to
a native folded conformation of the structure. Assuming it to be possible, I
thought of using g_rms;

g_rms -f native-folded.gro -s topol.tpr

Then I get the same error message:

WARNING: topology has 497 atoms, whereas trajectory has 491

Program g_rms, VERSION 4.5.1
Source code file: mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (491).

Thing is that both the topology and the trajectory are treated equally at
the pdb2gmx step. So how can it be?

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