"Invalid vsites3 type 0" error in gromacs

GROMACS version: 2020.1
GROMACS modification: Yes/No

Getting “Invalid vsites3 type 0” error in Gromacs after command “gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr”

Please suggest solution for this.


Hi Ashish,

this is a bit hard to see just from the post - something is broken when trying to generate virtual sites for your system.

This might be a mix-up of files or some odd virtual site definitions you are trying to apply? Maybe some renaming in the topology or your input file?

It’s helpful if you post a bit more information on how you set up the system up to this stage.

Hi Cblau,

Thanks… I understood the problem that it was because of some changes in original file.

Now, I am trying with fresh files but it is showing me an error with my .itp file and that error is:
“ERROR 1 [file unk.itp, line 427]:
Duplicate atom index (25) in virtual_sites3”

and when I see my .itp file, I found there,

[ virtual_sites3 ]
; Site from funct a d
** 47 28 25 25 2 0 -0.164**

[ exclusions ]
; ai aj
** 28 47 1**
** 47 25 1**
** 47 24 1**
** 47 26 1**
** 47 23 1**
** 47 27 1**
** 47 45 1**
** 47 46 1**

I am performing a protein-ligand MD study, an this is observed in my ligand.itp file. Also my ligand contains ONE CHLORINE atom.

please suggest me how to solve this problem.

Am I correct to assume you are using CGenFF, which include a lone pair for its halogen atom? If so, you’ve used an outdated conversion script that was designed for version 2016 of GROMACS (and prints a very verbose caveat about how you have to use the topology). Please get the new version of the conversion script from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs and re-create the topology. Version 2020 of GROMACS supports the correct virtual site construction without the hack we used years ago.

Thanks Justin… It worked and now able to run my job correctly.