[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
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