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

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 7 11:52:09 CET 2011

Sergio Manzetti wrote:
> 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).

Either (1) you're not saving the right atoms during the simulation (xtc-grps) or 
(2) you're choosing to analyze a non-existent group with g_rms, or a combination 
of both.  For better diagnostics, provide your .mdp file, a description of your 
system, and your g_rms command line.

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

pdb2gmx only deals with coordinate files in order to produce the topology.  Your 
trajectory is irrelevant here, but if you've somehow tried to manipulate your 
trajectory or its contents with pdb2gmx, then you can be sure that this is 
what's causing your error.


> Sergio


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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