Error parameters for dihedral type 9

User discussions
1

GROMACS version:2024
GROMACS modification: Yes/No
Hello,
I followed all the instruction of tutorial of GROMACS to setup MD similation for protein with my ligand. However, during the 1st step of adding ion, when I run this command lines
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

I encountered these error

Command line:

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘title’

Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file ions.mdp]:

With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

that with the Verlet scheme, nstlist has no effect on the accuracy of

your simulation.

Setting the LD random seed to 1966243839

ERROR 1 [file mbp.prm, line 25]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 2 [file mbp.prm, line 26]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 3 [file mbp.prm, line 27]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 4 [file mbp.prm, line 30]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 5 [file mbp.prm, line 31]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 6 [file mbp.prm, line 32]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 7 [file mbp.prm, line 35]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 8 [file mbp.prm, line 36]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 9 [file mbp.prm, line 37]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

ERROR 10 [file mbp.prm, line 38]:

Encountered a second block of parameters for dihedral type 9 for the same

atoms, with either different parameters and/or the first block has

multiple lines. This is not supported.

Generated 167799 of the 167910 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 1

Generated 117432 of the 167910 1-4 parameter combinations

ERROR 11 [file mbp.itp, line 5]:

moleculetype MBP is redefined

There was 1 NOTE

-------------------------------------------------------

Program: gmx grompp, version 2024.4-EasyBuild_4.9.4

Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1518)

Fatal error:

There were 11 errors in input file(s)

Can anyone give me instructions or suggestions how to fix it ?
Thanks

2

This looks like an issue caused by the force field files. What forcefield are you using and where did you get the files from?

3

I used charmm36-jul2022.ff

4

I got the .str file from CGFEN server after upload .mol2 file. Then I follow the instruction to use this command line to get mbp_ini.pdb mbp.prm mbp.top mbp.itp file
python cgenff_charmm2gmx.py MBP MBP_fix.mol2 MBP.str charmm36-jul2022.ff

5

I have never used cgfen, so I don’t know how this works. The charmm36-jul2022.ff package does not contain an mbp.prm file. There is clearly an issue in the mbp.prm file. Maybe you are lucky that the combination of atom types for this dihedral do not occur in your system, then you can remove the problematic lines.

6

Hi Hess,

I found the issue. It turns out that there is double line of include ligand in my topology file that causes the issues. I remove the duplicate line. It’s good now.