Amber to Gromacs file conversion and topol.top modification

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1

GROMACS version: GROMACS - gmx pdb2gmx, 2023.3-conda_forge
GROMACS modification: No
Here post your question
Experts.
I am new Gromacs user.

For the ligand BEJ, I have used amber parmchk2 to create the corresponding BEJ.frcmod file.
From this was generated BEJ.prmtop BEJ.inpcrd with tleap. This was then converted to

  • BEJ_GMX.top
  • BEJ_GMX.gro
    for simulation with a protein.

For the following command
!gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Fatal error:
Syntax error - File BEJ_GMX.top, line 3
Last line read:
‘[ defaults ]’
Invalid order for directive defaults

Are my file types correct for tool.top and how do I fix this error? I see this error documented but have no clue as to the resolution.

Here is my updated topol.top file

; File ‘topol.top’ was generated
; By user: ralph (501)
; On host: Ralphs-MacBook-Pro.local
; At date: Wed Jan 24 12:33:10 2024
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2023.3-conda_forge (-:
;
; Executable: /Users/ralph/anaconda3/bin.SSE2/gmx
; Data prefix: /Users/ralph/anaconda3
; Working dir: /Users/ralph/Documents/1ec2-run3
; Command line:
; gmx pdb2gmx -f 6czo4f22w2.pdb -o 1EC2_processed.gro -ter -ignh
; Force field was read from the standard GROMACS share directory.
;

; Include forcefield parameters
#include “amber99sb.ff/forcefield.itp”

; Include chain topologies
#include “topol_Protein_chain_A.itp”
#include “topol_Protein_chain_B.itp”

; Include ligand topology *************** ← I added this
#include “BEJ_GMX.top”

; Include water topology
#include “amber99sb.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 “amber99sb.ff/ions.itp”

; Include ligand parameters **************** ← I added this
#include “BEJ_GMX.gro”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
BEJ 1
SOL 10474

Regards

2

Hello, @RRRoberts

You should check your “BEJ_GMX.top” file and remove ‘[ defaults ]’ from this file. I think its line duplicates the information from the amber99sb.ff/forcefield.itp.

3

Yel21,
I have corrected that error to the BEJ_GMX.top file. I have re-run gmx grompp.
The current error is the following
“file BEJ_GMX.gro, line 1]:
Atomtype created not found”

Regards,…

4

These lines should not be in the topology file (topol.top):

; Include ligand parameters **************** ← I added this
#include “BEJ_GMX.gro”