# Error with virtual sites **URL:** \ **Category:** User discussions\ **Created:** [November 18, 2020, 1:48pm UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111 "2020-11-18T13:48:08Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\ **Post date:** [November 18, 2020, 1:48pm UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/1 "2020-11-18T13:48:08Z")
GROMACS version: 2020.1 GROMACS modification: No Hi all, I am trying to set virtual sites (VS) located at the COM of water TIP3P water molecules. However, I get the error with `grompp`: ``` ERROR 1 [file VS-water_mapping.itp, line 121]: The total mass of the construting atoms is zero ``` (The error message has a typo, btw). Water coordinates mapped are: ``` (...) 114TIP3 OH2 340 2.512 2.491 2.441 114TIP3 H1 341 2.606 2.472 2.435 114TIP3 H2 342 2.473 2.410 2.474 (...) ``` and the line in the mapping .itp file is: ``` #define mapping virtual_sitesn [mapping] (...) 6955 2 340 341 342 (...) ``` The masses of the atoms are well defined in the force field. Any thoughts? Thanks in advance. Best -Yasser ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [November 18, 2020, 7:40pm UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/2 "2020-11-18T19:40:51Z")
Hi, Maybe the problem is in the order in which the files are included in the topol.top Is the water .itp included before VS-water\_mapping.itp? Kind regards Alessandra ---
**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\ **Post date:** [November 19, 2020, 8:29am UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/3 "2020-11-19T08:29:42Z")
Hi Alessandra, Thank you for your reply. > [@alevilla](#): > > Is the water .itp included before VS-water\_mapping.itp? Yes. Bellow is a fragment of my `.top` file. ``` ; Include forcefield parameters #include "./FF/forcefield.itp" ; Restrained water #include "./FF/restrained_water.itp" (...) ; Include mapping of VS onto restrained waters #include "./FF/VS-water_mapping.itp" [system] ; Name Waters and VSs [molecules] ; Compound #mols TP3R 137 (...) VS 137 ``` That is also the order in my `.gro` file. The restrained waters come first and the VS are at the end of the file. The VS are defined under the [atomtypes] directive in `forcefield.itp` as: ``` [atomtypes] ; type atnum mass charge ptype sigma epsilon (...) VS 0 0.0000 0.00 A 0.0 0.0 ``` Best, -Yasser ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [November 19, 2020, 9:18am UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/4 "2020-11-19T09:18:50Z")
Hi, Thank you. From the data you sent I can not see where you include the water topology. Your water is called TP3R. Thus water topology looks like [moleculetype] ; molname nrexcl TP3R 2 [atoms] … Is this before the virtual site definition? Second, you can check that the atom types of the TP3R (not atom name) are properly defined (with a mass) in the ffnonbonded.itp. I hope it helps Alessandra ---
**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\ **Post date:** [November 19, 2020, 9:42am UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/5 "2020-11-19T09:42:23Z")
Hi Alessandra, Yes, the TP3R topology (TP3R is a just a name I use to define restrained TIP3 waters) is: ``` [moleculetype] ; name nrexcl TP3R 2 [atoms] ; nr type resnr residu atom cgnr charge mass 1 OT 1 TIP3 OH2 1 -0.834000 15.9994 2 HT 1 TIP3 H1 2 0.417000 1.0080 3 HT 1 TIP3 H2 3 0.417000 1.0080 (...) ``` This topology is included before the VS definition. The atom types are defined in a “mini”-`forcefield.itp` as: ``` [atomtypes] ; name at.num mass charge ptype sigma epsilon HT 1 1.0080 0.417 A 4.00013524445e-02 1.924640e-01 OT 8 15.9994 -0.834 A 3.15057422683e-01 6.363864e-01 VS 0 0.0000 0.00 A 0.0 0.0 (...) ``` Best, -Yasser ---
**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:** [November 19, 2020, 10:37am UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/6 "2020-11-19T10:37:20Z")
You can’t use global atom numbers in the virtual site definition. The only valid options are the atom numbers in the `[moleculetype]` definition (which must also include the virtual site). So you need to add the VS as atom 4 in the TP3R definition and then ``` [virtual_sitesn] 4 2 1 2 3 ``` This means the use of the virtual site applies globally to anything defined as T3PR. ---
**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\ **Post date:** [November 19, 2020, 3:04pm UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/7 "2020-11-19T15:04:11Z")
Dear Justin, Thank you for your reply. I just realized that by inspecting the file `tip4p.itp` (in charmm36-jul2020.ff) which contains a virtual site. So, in analogy with this, I modified my setup as: “mini”-`forcefield.itp`: ``` [atomtypes] ; name at.num mass charge ptype sigma epsilon HT 1 1.0080 0.417 A 4.00013524445e-02 1.924640e-01 OT 8 15.9994 -0.834 A 3.15057422683e-01 6.363864e-01 VS3 0 0.0000 0.00 A 0.0 0.0 (...) ``` `TP3R.itp`: ``` [moleculetype] ; name nrexcl TP3R 2 [atoms] ; nr type resnr residu atom cgnr charge mass 1 OT 1 TIP3 OH2 1 -0.834000 15.9994 2 HT 1 TIP3 H1 1 0.417000 1.0080 3 HT 1 TIP3 H2 1 0.417000 1.0080 4 VS3 1 TIP3 VS 1 0.000000 0.0000 [settles] ; OW funct doh dhh 1 1 9.572000e-02 1.513900e-01 [exclusions] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [virtual_sitesn] ; vs type_com mapped_atoms 4 2 1 2 3 ``` It’s that correct? Best -Yasser ---
**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:** [November 19, 2020, 7:38pm UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/8 "2020-11-19T19:38:48Z")
Looks reasonable. Try it and see :) ---
**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\ **Post date:** [November 20, 2020, 5:21pm UTC](https://gromacs.bioexcel.eu/t/error-with-virtual-sites/1111/9 "2020-11-20T17:21:58Z")
It worked! Thanks