[gmx-users] Simulation of membrane protein
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 31 17:13:03 CET 2011
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"
> ; 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
> 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
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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