[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

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

Position restraints can only be applied on a [moleculetype] basis.  Thus, order 
matters a lot, and the whole system cannot be restrained in one file.  See the 
example here:

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

As it stands now, the topology you've shown tries to apply lipid position 
restraints after the ions have been #included, which makes no sense at all.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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