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

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207>\
**Category:** User discussions\
**Tags:** grompp, mdrun\
**Created:** [November 26, 2021, 8:18am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207 "2021-11-26T08:18:45Z")\
**Posts on this page:** 14\
**Page:** 1

<div class="post-metadata">

**Author:** ![aldowanandy](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aldowanandy/32/1167_2.png) [@aldowanandy](https://gromacs.bioexcel.eu/u/aldowanandy)\
**Post date:** [November 26, 2021, 8:18am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/1 "2021-11-26T08:18:45Z")

</div>

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](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 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)

---

<div class="post-metadata">

**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [November 26, 2021, 6:43pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/2 "2021-11-26T18:43:07Z")

</div>

You don’t have required parameter for molecule SIN

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<div class="post-metadata">

**Author:** ![aldowanandy](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aldowanandy/32/1167_2.png) [@aldowanandy](https://gromacs.bioexcel.eu/u/aldowanandy)\
**Post date:** [January 7, 2022, 3:42pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/3 "2022-01-07T15:42:14Z")

</div>

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

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<div class="post-metadata">

**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [January 7, 2022, 3:44pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/4 "2022-01-07T15:44:12Z")

</div>

Follow Protein\_ligand tutorial. How did you parameterised SIN molecule?

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<div class="post-metadata">

**Author:** ![aldowanandy](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aldowanandy/32/1167_2.png) [@aldowanandy](https://gromacs.bioexcel.eu/u/aldowanandy)\
**Post date:** [January 7, 2022, 3:53pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/5 "2022-01-07T15:53:15Z")

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I use CHARMM General Force Field server

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [January 8, 2022, 11:36am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/6 "2022-01-08T11:36:49Z")

</div>

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](http://www.mdtutorials.com/gmx/complex/index.html)

---

<div class="post-metadata">

**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\
**Post date:** [April 20, 2023, 1:16am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/7 "2023-04-20T01:16:10Z")

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

```auto
  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](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](https://drive.google.com/drive/folders/19yWX-FtgDBloOGCevbep82fnqvr7otco?usp=share_link)

Thanks

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 20, 2023, 2:32am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/8 "2023-04-20T02:32:25Z")

</div>

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

```auto
; 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.

---

<div class="post-metadata">

**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\
**Post date:** [April 20, 2023, 2:47am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/9 "2023-04-20T02:47:46Z")

</div>

@jalemkul Thank you for looking into it.

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

> [@shivam1](#):
>
> ```auto
> 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
> 
> ```

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 20, 2023, 3:00am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/10 "2023-04-20T03:00:05Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\
**Post date:** [April 21, 2023, 2:01am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/11 "2023-04-21T02:01:03Z")

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@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

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 21, 2023, 2:12am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/12 "2023-04-21T02:12:03Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\
**Post date:** [April 21, 2023, 5:49am UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/13 "2023-04-21T05:49:46Z")

</div>

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.

```auto
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

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 21, 2023, 12:53pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-there-were-2-errors-in-input-file-s/3207/14 "2023-04-21T12:53:34Z")

</div>

> [@shivam1](#):
>
> 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?

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.