[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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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