# Small molecule chlorines **URL:** \ **Category:** HADDOCK\ **Created:** [August 21, 2023, 12:42pm UTC](https://ask.bioexcel.eu/t/small-molecule-chlorines/4458 "2023-08-21T12:42:26Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![JHlatt](https://avatars.discourse-cdn.com/v4/letter/j/5f9b8f/32.png) [@JHlatt](https://ask.bioexcel.eu/u/JHlatt)\ **Post date:** [August 21, 2023, 12:42pm UTC](https://ask.bioexcel.eu/t/small-molecule-chlorines/4458/1 "2023-08-21T12:42:26Z")
Hi, I’m trying to dock a small molecule that has 2 chlorine atoms within it. Whenever I run webserver the resulting docked small molecule always swaps these chlorines for carbon atoms. I have tried to edit the input pdb text file a few times to see if it will accept them as chlorines but haven’t had any luck. (Below is currently what they look like in the text file. HETATM 1 CL1 UNK 0 1.235 3.281 0.000 0.00 0.00 CL HETATM 2 CL2 UNK 0 3.660 -1.471 -0.000 0.00 0.00 CL If you can advise me where I’m going wrong that would be great. Thank you ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [August 21, 2023, 2:00pm UTC](https://ask.bioexcel.eu/t/small-molecule-chlorines/4458/2 "2023-08-21T14:00:32Z")
Chlorine atoms are not supported - sorry ---
**Author:** ![Bahaa\_Ali](https://avatars.discourse-cdn.com/v4/letter/b/47e85d/32.png) [@Bahaa\_Ali](https://ask.bioexcel.eu/u/Bahaa_Ali)\ **Post date:** [August 25, 2026, 1:09pm UTC](https://ask.bioexcel.eu/t/small-molecule-chlorines/4458/3 "2026-08-25T13:09:23Z")
is it still unsupported? or there is a problem in my pdb format? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [August 25, 2026, 5:41pm UTC](https://ask.bioexcel.eu/t/small-molecule-chlorines/4458/4 "2026-08-25T17:41:16Z")
Still unsupported