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:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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