[gmx-users] lipid restrain

RINU KHATTRI nickname.mittu at gmail.com
Sat Jul 26 08:45:40 CEST 2014


hello every one
i am working on complex with POPC membrane i want to use position restrain
in lipid but it is not working it's give error
 file lipid_posre.itp, line 57 ]:
Atom index (53) in position_restraints out of bounds (1-52).
this probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
last line sof my topology file is
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand topology
#include "epi.itp"

; Include Position restraint file for UNK
#ifdef DPOSRES_UNK
#include "posre_unk.itp"
#endif

; Include POPC side chain topology
#include "popc.itp"

; Include Position restraint file for lipid
#ifdef DPOSRES_LIPID
#include "lipid_posre.itp"
#endif

; Include water topology
#include "gromos43a1_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif
[moleculetype]
POPC
#ifdef DPOSRES_LIPID
[ position_restraints ]
; i  funct  fcx    fcy    fcz
   8    1    1000000   1000000   100000   ; restrains to a point x,y,z

#endif

; Include topology for ions
#include "gromos43a1_lipid.ff/ions.itp"

[ system ]
; Name
Displayed atoms in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
UNK    1
POPC    122
SOL    9410
CL    15
my min.mdp is
define        = -DPOSRES_LIPID -DPOSRES -DPOSRES_UNK   ;position restrain
on protein  ligand and POPC


More information about the gromacs.org_gmx-users mailing list