"Invalid vsites3 type 0" error in gromacs

User discussions
1

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.

Thanks…
Ashish

2

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.

3

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.

4

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 If so, you’ve used an outdated conversion script that was designed for version 2016 of GROMACS (and prints a very verbose caveat about how you have to use the topology).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.

5

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