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.