Error assembling .tpr file from .mdp file for energy minimization (solved)

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1

GROMACS version: 2023.2
GROMACS modification: No
device: M1 macbook (arm not intel)

Hi everyone,

I have been following this tutorial from Virginia Tech and ran into an error at the energy minimization step. After downloading the MDP file minum.mdp and adding it to my directory that I have been using so far and running the command gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr, I get the following result:

Command line:
  gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr


ERROR 1 [file minim.mdp, line 4]:
  No '=' to separate .mdp parameter key and value was found on line:
  'minimization)'


ERROR 2 [file minim.mdp, line 6]:
  No '=' to separate .mdp parameter key and value was found on line:
  '1000.0 kJ/mol/nm'


ERROR 3 [file minim.mdp, line 9]:
  No '=' to separate .mdp parameter key and value was found on line:
  'perform'


ERROR 4 [file minim.mdp, line 12]:
  No '=' to separate .mdp parameter key and value was found on line:
  'calculate the interactions'


ERROR 5 [file minim.mdp, line 14]:
  No '=' to separate .mdp parameter key and value was found on line:
  'long range forces'


ERROR 6 [file minim.mdp, line 17]:
  No '=' to separate .mdp parameter key and value was found on line:
  'grid)'


ERROR 7 [file minim.mdp, line 19]:
  No '=' to separate .mdp parameter key and value was found on line:
  'interactions'


ERROR 8 [file minim.mdp, line 23]:
  No '=' to separate .mdp parameter key and value was found on line:
  'dimensions'

Ignoring obsolete mdp entry 'ns_type'

-------------------------------------------------------
Program:     gmx grompp, version 2023.2
Source file: src/gromacs/fileio/readinp.cpp (line 246)

Fatal error:
There were 8 errors in input file(s)

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

I am not sure how to proceed from here. I am a GROMACS noob. The tutorial is from 2018. Is it possible that the mdp file is outdated?

Any insight would be appreciated. Please let me know if I should provide more details. I will gladly do so.

Thanks.

2

The errors suggest something really broken within the .mdp file itself. If you previously ran grompp to produce the .tpr input for genion, this means your installation is functional and simple tasks like this should work. If you have opened the file with some kind of rich-text editor, delete it and get a fresh copy. The fact that it isn’t recognizing = delimiters is something I’ve literally never seen before in this tutorial (which is going on 15 years online…)

4

Thank you for the response! Previously, I simply clicked the link to the .mdp file which prompted the file to load in my browser, and from there I copy and pasted the text into a .mdp file. I solved this by instead obtaining the file directly via wget.

Also, are you the pi from the lab that made these tutorials? Kudos to you guys! Thank you so much for your tutorials! I greatly appreciate them.

5

Right click → Save As should also do the trick. Likely the copy-paste process added some extraneous formatting characters or something. You can always check the contents of the file with a plain-text editor like Emacs or VIM.

I wrote the tutorials as a grad student and have been maintaining them ever since :)