[gmx-users] KALP in DPPC tutorial reg

[Justin Lemkul]

On 10/14/13 2:44 AM, Sathya wrote:
> Hi,
>
> I'm doing the KALP-15 IN DPPC through the Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
>
> 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


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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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