# Halogenated organic compounds and charmm36 **URL:** \ **Category:** User discussions\ **Created:** [November 28, 2023, 4:03pm UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743 "2023-11-28T16:03:49Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![mario.pagano](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mario.pagano](https://gromacs.bioexcel.eu/u/mario.pagano)\ **Post date:** [November 28, 2023, 4:03pm UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743/1 "2023-11-28T16:03:49Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I have a benzotriazole with two bromines and two iodines bound to the benzene ring. The bonds appear in the .pdb and .mol2 format, but after parametrization with cgenff or charmm-gui, both halogens are misrepresented as “dots” (upper picture attached, lig\_ini.pdb) or weird bonds occur (lower picture attached, ligandrm.pdb) respectively. Does anyone suggest how to sort it out? Very grateful to anyone who can help out Mario ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [November 29, 2023, 8:20am UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743/2 "2023-11-29T08:20:10Z")
Dear @mario.pagano What do you mean the bonds appear and disappear? While visualizing the molecules with something like VMD? Keep in mind that bonds are hard-coded in the topology (the .itp file of the molecule), they can’t disappear as long as they are reported there. This is probably due to the visualizer you are using, for example generally VMD guesses the bonds by looking at the structure file (see [here](https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node23.html)). As such, you probably don’t see them but they are there (if they are reported in the .itp files), same for those seeming weird. Whether then the visualizer failing to guess the bonds may indicate an error in the parametrization or not, there I don’t know, but for sure that’s a good reason to double check what is going on in your topology generation. ---
**Author:** ![mario.pagano](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mario.pagano](https://gromacs.bioexcel.eu/u/mario.pagano)\ **Post date:** [November 29, 2023, 2:03pm UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743/3 "2023-11-29T14:03:05Z")
This is what I see in the charmm-gui server visualization application and by using chimera after parametrization with cgenff (charm36 ff). ![Screenshot_20231129-144628_Chrome](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/660bf6d9a0f23d8a042eecb774a7caa1594cb6a8.jpeg) ![Screenshot_20231129-144557_Chrome](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1cd7871c158be482ffa95b93d96471913b5e652f.jpeg) Dr Lemkul suggested that it is a visualization issue due to the length of the bonds between halogens and carbons that is misinterpreted by the software. In the ini.pdb and lig.str generated by genff a fre atoms are listed as LP, by which “sigma holes” are defoned in the halogen bonds. May this visualization issue jeopardize the whole simulation? ---
**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 29, 2023, 2:14pm UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743/4 "2023-11-29T14:14:53Z")
The visualization has nothing to do with the integrity of the simulation. Also note that there are no topological bonds between lone pairs and halogens; they are virtual sites and are constructed as rigid entities. ---
**Author:** ![mario.pagano](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mario.pagano](https://gromacs.bioexcel.eu/u/mario.pagano)\ **Post date:** [November 29, 2023, 10:06pm UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743/5 "2023-11-29T22:06:07Z")
Thanks for the explanation. But if I need to extract a frame after the simulation, can I get a picture with all the bonds visible by using vmd, pymol, chimera or else? Thanks you Mario ---
**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:** [December 7, 2023, 2:44pm UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743/6 "2023-12-07T14:44:01Z")
Most programs allow you to manually add a bond for visualization purposes. Check the specific syntax of the program you’re trying to use. I know this is simple in PyMOL with the `bond` command. ---
**Author:** ![mario.pagano](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mario.pagano](https://gromacs.bioexcel.eu/u/mario.pagano)\ **Post date:** [December 10, 2023, 4:21pm UTC](https://gromacs.bioexcel.eu/t/halogenated-organic-compounds-and-charmm36/7743/7 "2023-12-10T16:21:33Z")
Thanks. It worked