[gmx-users] Position restraint on DPPC lipid bilayer

[Justin Lemkul]

On 4/7/17 1:20 AM, Sithara Perera wrote:
> Hi!,
>
>  I' making a 512 DPPC bi-layer out of 128 bilayer available in
> http://www.cgmartini.nl. The force field used is martini.
>
>  But once the energy minimization is done, the bi-layer crashes and
> accumulates to  globules.
>
>  So I made an position.itp file using the command
>
>
> gmx genrestr -f dppc221.gro -n test.ndx -o lipid_posre.itp -fc 1000 1000
> 1000
>
> And included in the topology file.
>
> Topology file also include
>
> include "martini_v2.0.itp"
> #include "martini_v2.0_lipids.itp"  from martini as well.
>
>
>
>  But then when the command
>
> gmx grompp -f minim.mdp -c dppc221.gro -p dppc_bilayer.top -o em2.tpr
>
> is given , following error occurs.
>
> Fatal error:
> [ file posre.itp, line 29 ]:
> Atom index (25) in position_restraints out of bounds (1-24).
> 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.
>
>
> How can I fix this?
>

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

As a rule of thumb, if you're ever passing a coordinate file containing multiple 
molecules to genrestr, you're probably going to get an incorrect restraint 
topology (note the warnings in the help text).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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