CHARMM Force Field Missing Script Files

User discussions
1

GROMACS version: 2023.3
GROMACS modification: No
Here post your question

Dear all,

I’m getting the following error at ion addition step to my protein-ligand complex with the command:

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

ERROR 1 [file lig.itp, line 474]:
  Duplicate atom index (35) in virtual_sites3

As I scrolled through the forum, this error comes from the usage of old version of the Cgenff script as stated here: Link

The script I used for the generation of my .itp file is cgenff_charmm2gmx_py2. I intended to download another script to fix this error from Mackerell Lab’s website and it seems the website is not active anymore, therefore I couldn’t find the alternative version of these scripts on somewhere else.

Any help would be appreciated.

2

If that’s just a single entry, you can delve into how virtual sites are constructed and what format is required to set them up in Gromacs, and figure out how it should be fixed for your molecule.

3

Please use the Python3 version of the script. It is the one that is more actively maintained. I changed the virtual site construction long ago. The duplicate entry strategy was essentially exploiting a bug in version 2016 but is no longer valid. There is a new way to build virtual sites as needed by CGenFF, which was added to GROMACS version 2020.