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