GROMACS version: GROMACS - gmx pdb2gmx, 2023.3-Ubuntu_2023.3_1ubuntu3
GROMACS modification: Yes/No
I am new to MD and GROMACS. I am performing molecular dynamics (MD) simulations for a protein-ligand complex, where the protein is a tetramer (chains A, B, C, and D). The ligand is docked to chain A.
During the step of adding the ligand parameters and topolgy to the system topology, I opened the topol.top file and found it to be different from the tutorial example. As a result, I was unsure where to paste the following two:
; Include ligand topology #include “jz4.itp”
; Include ligand parameters #include “jz4.prm”
Here is the toplo.top file:
;
; File ‘topol.top’ was generated
; By user: unknown (0)
; On host: LAPTOP-3GKP069M
; At date: Tue Jan 7 23:52:28 2025
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:
;
; Executable: /usr/bin/gmx
; Data prefix: /usr
; Working dir: /mnt/c/Users/alaas/Desktop/EMPA_MD
; Command line:
; gmx pdb2gmx -f REC.pdb -o REC_processed.gro -ter
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include “charmm27.ff/forcefield.itp”
; Include chain topologies
#include “topol_Protein_chain_A.itp”
#include “topol_Protein_chain_B.itp”
#include “topol_Protein_chain_C.itp”
#include “topol_Protein_chain_D.itp”
; Ligand position restraints
#ifdef POSRES
; Include water topology
#include “charmm27.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 “charmm27.ff/ions.itp”
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1