[gmx-users] KALP in DPPC tutorial reg
jalemkul at vt.edu
Mon Oct 14 13:40:58 CEST 2013
On 10/14/13 2:44 AM, Sathya wrote:
> 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
> LOOP :
> 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
You created the restraint file wrong. Please follow the tutorial exactly.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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