[gmx-users] Problem in g_rms

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 27 05:28:18 CET 2010

On 27/01/10 15:11, rituraj purohit wrote:
> I want get rmsd deviation between NMR structure and the simulated
> result, but i am getting following error in following command.
> g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg
> WARNING: topology has 50772 atoms, whereas trajectory has 22899
> -------------------------------------------------------
> Program g_rms, VERSION 4.0.5
> Source code file: mshift.c, line: 103
> Fatal error:
> Molecule in topology has atom numbers below and above natoms (22899).
> You are probably trying to use a trajectory which does not match the
> first 22899 atoms of the run input file.
> You can make a matching run input file with tpbconv.
> -------------------------------------------------------
> I want to analyze RMSD of backbone atoms. They mention about tpbconv,
> How i can use it to sort it out ?
> Please help me..

Please help yourself, also :-) tpbconv -h is the best starting point, 
followed by cautious trial and error.


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