[gmx-users] KALP in DPPC tutorial reg

Sathya bti027.2008 at gmail.com
Mon Oct 14 08:44:47 CEST 2013


I'm doing the KALP-15 IN DPPC through the Justin's tutorial

After generating the new position restrain file, I start to energy
minimization to get the correct area per lipid. As below:

 Scale the lipid positions by a factor of 4:
     perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

     Energy minimization with restrained protein
     grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
-maxwarn 1.

 after using the above command I got error like this

Fatal error:
[ file strong_posre.itp, line 143 ]:Atom index (139) in position_restraints
out of bounds (1-138).
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.

Please help me how to  solve  this

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