Hello everyone, I am trying to simulate the protein-ligand complex with Zn ion but during solvation i am getting the following error:
Fatal error:
Syntax error - File LIG.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
I tried many ways but not able to solve this issue
My topology file
Topology file:
; Include forcefield parameters
#include "amber03.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"
; Include ligand topology
#include "LIG.itp"
; Include water topology
#include "amber03.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber03.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Ion_chain_A2 1
LIG 1
SOL 27420
I also placed ligand itp file below forcefield parameters but it doesn't work. If you guys have any idea how to tackle this problem please help me. Thank you.
Hello,
I checked the topol.top where the forcefield parameters lines in top while in older version the force field parameters defines in last section of topol.top
so you have to define your ligand .itp in below forcefield parameters lines.
ex.
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2020.4 (-:
;
; Executable: /apps/GROMACS/2020.4/bin/gmx_mpi
; Data prefix: /apps/GROMACS/2020.4
; Working dir:
; Command line:
; gmx_mpi pdb2gmx -f protein.pdb -o complex.gro -ignh
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "charmm36-feb2021.ff/forcefield.itp"
#include "AW_GMX.itp"
.....
[ molecules ]
; Compound #mols
Protein_chain_A 1
LIG 1
SOL 13404
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