[gmx-users] mismatch atoms?

Albert mailmd2011 at gmail.com
Wed Aug 29 08:22:55 CEST 2012

   I am trying to extract one frame of my simulation results by commands:

trjconv -f md.trr -s tuned.tpr -o md.xtc -pbc mol -timestep 100 -n out.ndx
trjconv -f md.xtc -s tuned.tpr -fit rot+trans -o out.pdb -dump 
133000.000 -n out.ndx

However, it said:

Fatal error:
Index[31715] 31716 is larger than the number of atoms in the
trajectory file (31715). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Does anybody has any advices?

thank you very much

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