[gmx-users] inflate gro

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 20 05:05:31 CEST 2011

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."
> I wonder if any one could help me with it.

The error message explains pretty clearly what's wrong.  A [position_restraints] 
block can only apply to the [moleculetype] that contains it.  Yours is somehow 
out of order.  The tutorial has specific instructions on how to organize the 
topology appropriately:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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