[gmx-users] Problem in Molecular dynamics of ligand protein complex in POPC lipid

neha bharti nehabharty123 at gmail.com
Tue Jul 22 08:13:51 CEST 2014

Hello All

I an trying molecular dynamics simulation of ligand protein complex in popc
lipid with charmm36 force field and also follow Justin tutorial. But in
that tutorial its only for protein not for ligand protein complex. I also
took help of Justin protein-ligand complex tutorial. But while performing
energy minimization step in  "Pack the lipids around the protein " its
giving following error:

Fatal error:
Syntax error - File cyc.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

my topology file is :

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

; Strong position restraints for InflateGRO
#include "strong_posre.itp"

; Include ligand topology
#include "cyc.itp"

; Ligand position restraints
#ifdef POSRES
#include "posre_cyc.itp"

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

; Include water topology
#include "charmm36.ff_lipid/tip3p.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "charmm36.ff_lipid/ions.itp"

[ system ]
; Name
Protein in Lipid

[ molecules ]
; Compound        #mols
Protein             1
LIG            1
POPC                128

I also check my changing the position of LIG and POPC like

POPC    128
LIG     1

But it still giving the same error..

Can any one please help me out for this..

Is there any tutorial for ligand protein complex in lipid???

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