Fatal error: There were 2 errors in input file(s)

User discussions
,
1

GROMACS version: 2020.1
GROMACS modification: No
Here post your question : I found an error message like the one below after I tried the add ions step on my complex. (my .pdb protein was previously prepared to change the pH using Yasara). Can someone give me some advice? Thanks.

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 -510674674
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations

ERROR 1 [file sin.itp, line 331]:
No default Proper Dih. types

ERROR 2 [file sin.itp, line 344]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘SIN’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 48771]:
System has non-zero total charge: -12.000000
Total charge should normally be an integer. See
GROMACS - Gromacs
for discussion on how close it should be to an integer.

There were 2 notes

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)

Fatal error:
There were 2 errors in input file(s)

2

You don’t have required parameter for molecule SIN

3

thanks for your response, may I know how to add the required parameters for the SIN molecule? thank you

4

Follow Protein_ligand tutorial. How did you parameterised SIN molecule?

5

I use CHARMM General Force Field server

6

You probably forgot to #include the associated parameter file. If there are new parameters for the ligand, the server generates them and our conversion utility writes them to a separate file. This is addressed in my tutorial: Protein-Ligand Complex

7

@jalemkul
I have also the same error. Here is the full output.

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

Ignoring obsolete mdp entry 'ns_type'

NOTE 1 [file ./mdp_files/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 -545521671

Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 65937 of the 100128 1-4 parameter combinations

ERROR 1 [file jz4.itp, line 180]:
  No default Proper Dih. types


Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

Excluding 3 bonded neighbours molecule type 'JZ4'

Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 24632]:
  System has non-zero total charge: 6.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
  



There were 2 notes

-------------------------------------------------------
Program:     gmx grompp, version 2022.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2172)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I have generated ligand topology using ‘https://cgenff.umaryland.edu/userAccount/userLogin.php’ and cgenff_charmm2gmx_py3_nx2.py script as per your protocol.

Please find the associated files in the drive.
https://drive.google.com/drive/folders/19yWX-FtgDBloOGCevbep82fnqvr7otco?usp=share_link

Thanks

8

The solution is what I said above. In your case, you have a typo:

; Include ligand parameters
#include "jz4.prm

Once you close the quotes it should parse correctly, though I’m surprised you didn’t get a syntax error in the first place.

9

@jalemkul Thank you for looking into it.

I have rectified this typo but still shows the same error.

10

Try with the July 2022 release of the force field. It uses the same CGenFF version as the server that generated the JZ4 topology. Likely a parameter has been added to the core force field that wasn’t present in the version released in March 2019. Everything else (in terms of the tutorial) is functionally identical, though the topology may be slightly different, which is not a concern.

11

@jalemkul
Thank you for the suggestion. I am facing the same problem with other protein-ligand simulations following your protocol. I think recently (1-2 day before) they have updated something because my previous simulations were showing no error while adding ions.
Could you please provide me with the updated MDP files for using charmm36-july2022 or I can proceed with the old MDPs?

Regards

12

Nothing about the .mdp files in the tutorials depends on the force field version.

13

Thanks… Now it shows no error while using charmm36-jul2021. But in the equilibration step, while creating tc-grps it throws error as the index file has not Water_and_ions group.

Fatal error:
Group Water_and_ions referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

How to create them? or do we need to choose some other group for temperature coupling? Should I create them manually by combining SOD,CLA atoms with Water Atoms?

Or Can we proceed with the creating group for temperature coupling group for Protein_JZ4 and Water ie tc-grps = Protein_JZ4 Water

regards

14

This should be a default group (in the version for which the tutorial was written) but if not, you need to create it. There are ions in the system, you can’t ignore them and only couple the water to a thermostat.