[gmx-users] Invalid atom number 6415 in indexfile

[Justin A. Lemkul]

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

<snip>

> -------------------------------------------------------
> 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

-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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