[gmx-users] Simulation of membrane protein

[Mark Abraham]

On 1/11/2011 3:00 AM, James Starlight wrote:
> 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"
>
> #ifdef POSRES_LIPID
> #include "posre_lipid.itp"
> #endif
>
> ; System specifications
> [ system ]
> 128-Lipid DMPC Bilayer in water
>
> [ molecules ]
> ; molecule name nr.
> DPPC 64
> 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 
> "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.
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors

The text of the error is exactly right about what is wrong. Please read 
and take time to understand before firing off email. You will learn more 
and faster if you read and understand documentation relevant to a 
situation before asking questions, and you will use less of everyone 
else's volunteer time. Also, if you follow that link, you will find a 
worked example of fixing your problem.

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

It is often more profitable to understand why the error occurs, rather 
than guess at the form of the solution.

Mark

>
> James
>
> 2011/10/31 Justin A. Lemkul <jalemkul at vt.edu <mailto: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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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