[gmx-users] inflate gro

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 20 05:06:30 CEST 2011

On 20/07/2011 12:28 PM, Sweta Iyer wrote:
> Hi,
>   I am trying to use inflategro to efficiently insert my protein into lipid
> bilayer. I have been following the KALP-15 in DPPC tutorial to do so.
> However, after running the perl script for the first time, I am not able
> to perform energy minimisation. The error message that I get when I pre
> process my files for EM is as follows:
> "Fatal error:
> [ file strong_posre.itp, line 294 ]:
> Atom index (290) in position_restraints out of bounds (1-289).
> This probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule."

Either the script doesn't work, or you're not yet using it correctly. Do 
read over the documentation (again) and try following the tutorial again 
from the beginning.


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