[gmx-users] Invalid atom number 6415 in indexfile

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 21 21:00:37 CET 2009

Liu Shiyong wrote:
> Hi,
>  I got an error when do grompp:   The input PDB file comes from the 
> output of GROMACS by trajconv command.


> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: ../../../../src/kernel/readir.c, line: 838
> *Fatal error:
> Invalid atom number 6415 in indexfile*
> -------------------------------------------------------

Instead of screen dumps, it would be a lot more useful to see your .mdp file, as 
well as the command line (not output from) both grompp and trjconv.  Did you 
dump the frame from an .xtc file?  What did you specify in xtc-grps?



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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