[gmx-users] Problem in g_rms

rituraj purohit riturajpurohit at gmail.com
Wed Jan 27 05:11:35 CET 2010

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..

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