[gmx-users] Re: Molecule in topology has atom numbers below and above natoms

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jul 31 22:56:08 CEST 2012

Thales Kronenberger wrote
> Hello Everybody
> I'm running a production simulation of a kinase (after minimization
> and equilibration) and after concluded 20ns I got the following
> problem when I tryied to run g_rmsf
> "Fatal error:
> Molecule in topology has atom numbers below and above natoms (4005).
> You are probably trying to use a trajectory which does not match the
> first 4005 atoms of the run input file.
> You can make a matching run input file with tpbconv.
> For more information and tips for troubleshooting, please check the
> website at http://www.gromacs.org/Documentation/Errors"
> I insert ions in the PDB and ATP. My ion's topology were included as:
> "#include "WT_Other_chain_A2.itp", #include "WT_Other_chain_B2.itp"".
> I don't know if they're causing the trouble

They aren't. But like the error message says, until you know what the
coordinates in your trajectory file represent, and how that relates to the
run input file you gave to g_rmsf it will be a mystery.


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