[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Mon Oct 31 17:00:01 CET 2011

I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )

I've included this in the topology of the bilayer

; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

; Include ion topologies
#include "gromos53a6_lipid.ff/ions.itp"

#include "posre_lipid.itp"

; System specifications
[ system ]
128-Lipid DMPC Bilayer in water

[ molecules ]
; molecule name nr.
SOL              1193
SOL               690

Also I've tried to make posre for whole system ( large posres ) but it also
was finished with same error

Fatal error:
[ file posre_lipid.itp, line 6 ]:
Atom index (2) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What's most true for such multy system. Generate posre only for 1 part or
for whole system?


2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>

> James Starlight wrote:
>> Thanks, Justin
>> I'll test your program soon.
>> Today also I have some problems with generation of the posre for lipids
>> I have lipid bilayer in pdb. Then I selected one lipid molecule and move
>> it to  separate pdb and convert it to gro via editconf.
>> Than I've used genres and generate posre file for 1 lipid. Than I include
>> tis posre to topology of my bilayer
>> using gropt I obtain eror that I'm using wrong posre topology
>> Also I've tried to include posre.itp to my lipid.itp ( this file contain
>> link to posre on default) This run didnt produce any errors but as the
>> result posres have not been worked ( I obtained perturbed bilayer after
>> minimization)
>> How I can generate work posre for my bilayer to prevent perturbation
>> after equilibration or minimization ?
> Since posre.itp is the default name given to the protein position
> restraint file by pdb2gmx, the first step is to use a different name.
>  Then, you have to add the new #include statement in the correct location
> in the topology.  Presuming you do that, the lipids should be restrained in
> whatever manner you've specified.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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