# "Invalid vsites3 type 0" error in gromacs

**URL:** <https://gromacs.bioexcel.eu/t/invalid-vsites3-type-0-error-in-gromacs/379>\
**Category:** User discussions\
**Created:** [June 26, 2020, 6:15pm UTC](https://gromacs.bioexcel.eu/t/invalid-vsites3-type-0-error-in-gromacs/379 "2020-06-26T18:15:00Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![ashish](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@ashish](https://gromacs.bioexcel.eu/u/ashish)\
**Post date:** [June 26, 2020, 6:15pm UTC](https://gromacs.bioexcel.eu/t/invalid-vsites3-type-0-error-in-gromacs/379/1 "2020-06-26T18:15:00Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [June 30, 2020, 9:48am UTC](https://gromacs.bioexcel.eu/t/invalid-vsites3-type-0-error-in-gromacs/379/2 "2020-06-30T09:48:41Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![ashish](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@ashish](https://gromacs.bioexcel.eu/u/ashish)\
**Post date:** [July 7, 2020, 3:36pm UTC](https://gromacs.bioexcel.eu/t/invalid-vsites3-type-0-error-in-gromacs/379/3 "2020-07-07T15:36:52Z")

</div>

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.

---

<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:** [July 7, 2020, 3:49pm UTC](https://gromacs.bioexcel.eu/t/invalid-vsites3-type-0-error-in-gromacs/379/4 "2020-07-07T15:49:26Z")

</div>

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](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.

---

<div class="post-metadata">

**Author:** ![ashish](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@ashish](https://gromacs.bioexcel.eu/u/ashish)\
**Post date:** [July 7, 2020, 5:23pm UTC](https://gromacs.bioexcel.eu/t/invalid-vsites3-type-0-error-in-gromacs/379/5 "2020-07-07T17:23:29Z")

</div>

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