# X2top not generating listed interactions correctly **URL:** \ **Category:** User discussions\ **Tags:** forcefield, topology, x2top\ **Created:** [July 10, 2026, 12:02pm UTC](https://gromacs.bioexcel.eu/t/x2top-not-generating-listed-interactions-correctly/13593 "2026-07-10T12:02:23Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\ **Post date:** [July 10, 2026, 12:02pm UTC](https://gromacs.bioexcel.eu/t/x2top-not-generating-listed-interactions-correctly/13593/1 "2026-07-10T12:02:23Z")
GROMACS version: 2026.1 GROMACS modification: No Hi, I am trying to generate the topology for two refrigerant molecules (1233zd and 1234ze) using `gmx x2top`. These are my force field files: [workflow-refrigerants/example/refrigerants.ff at main · MicPellegrino/workflow-refrigerants · GitHub](https://github.com/MicPellegrino/workflow-refrigerants/tree/main/example/refrigerants.ff) And this is the call to x2top: ```auto gmx x2top -f HFO-1234zeE.gro -ff refrigerants -name HFO-1234zeE -o HFO-1234zeE.top -alldih -v ``` The configuration `.gro` file is the follwoing: ```auto LIGPARGEN GENERATED GRO FILE 9 1UNK F00 1 0.100 0.100 0.000 1UNK C01 2 -0.034 0.100 0.000 1UNK H02 3 -0.074 0.100 0.101 1UNK C03 4 -0.103 0.100 -0.114 1UNK C04 5 -0.251 0.100 -0.121 1UNK F05 6 -0.295 0.099 -0.249 1UNK F06 7 -0.304 -0.009 -0.060 1UNK F07 8 -0.305 0.209 -0.060 1UNK H08 9 -0.051 0.100 -0.209 2.50000 2.50000 2.50000 ``` The resulting bond, angle and dihedral parameters are inconsistent with the values in `refrigerants.ff`, for example: ```auto [bonds] ; ai aj funct c0 c1 c2 c3 1 2 1 1.340000e-01 4.000000e+05 1.340000e-01 4.000000e+05 2 3 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 2 4 1 1.330000e-01 4.000000e+05 1.330000e-01 4.000000e+05 4 5 1 1.480000e-01 4.000000e+05 1.480000e-01 4.000000e+05 4 9 1 1.080000e-01 4.000000e+05 1.080000e-01 4.000000e+05 5 6 1 1.350000e-01 4.000000e+05 1.350000e-01 4.000000e+05 5 7 1 1.360000e-01 4.000000e+05 1.360000e-01 4.000000e+05 5 8 1 1.360000e-01 4.000000e+05 1.360000e-01 4.000000e+05 ``` The bond distance bewteen 4 and 5 should be 0.1511 nm instead of 0.148. Where do these numbers come from? They seem completely arbitrary to me. Also, I assume that `c2` and `c3` are ignored since `funct=1`. However, `c1` (spring constant) seems set to a sort of default value and not the one specified in the FF files. As a side note, I wonder how `gmx x2top` can distinguish between atom types that are bonded to atoms with the same periodic table name. For example, I have two types of flourine atoms (`FCM` and `FCT`), the former bonded to a `CM` carbon (alone), while the latter bonded to a `CT` carbon (with other 2 `FCT` atoms). They differer in the partial charge and the non-bonded parameters. Since the `.n2t` file only calls for bonds to determine the topology (i.e. no angles or dihedrals), and the bond length is very similar, `x2top` mistakenly attributes the parameters of `FCM` to `FCT`. I hope my question is clear. You can have a look to my GitHub repo ([GitHub - MicPellegrino/workflow-refrigerants: Workflow for wettability and free energy simulations of refrigerants using GROMACS · GitHub](https://github.com/MicPellegrino/workflow-refrigerants.git)) to replicate the issue. Regards, Michele ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [July 23, 2026, 1:17pm UTC](https://gromacs.bioexcel.eu/t/x2top-not-generating-listed-interactions-correctly/13593/2 "2026-07-23T13:17:21Z")
I don’t think any information from the force field is used. The help text says that bond equilibrium distances are taken as the distances in the input coordinates.