The coordinates for the chlorine atom are there, the chlorine atom simply is not colored green, but gray like the carbon atoms.

- which viewer program are you using?

Click on the atom and see if it is called labelled correctly as chlorine.

Test if it is just an error in element to color mapping by selecting the element chlorine and explicitly coloring it green.

If the atom is indeed mis-identified as carbon:

- did you look at the pdbqt file in a text viewer?

If it is not a problem with the color assignment in the viewer, somewhere along the format conversions the chlorine (CL) has been mis-interpreted as carbon (C). As these files are fixed-format text files, so simply putting the atom name into the wrong text column can lead to errors. However, one would need to know exactly what you did with which program to find where the error occurred.

Thankyou Annemarie Honegger for quick response. I am using BIOVIA Discovery Studio Visualizer,(DSV) for visualization. If I label the atom as shown in image it is showing it as CL but not with green colour. Similarly, in text file also it showing as CL only. I am not sure is DSV considering it as CL or C.

The file looks OK to me, compared to other chlorine containing pdbqt files (e.g. https://www.cbligand.org/g/virus-ckb/job/w112 ). I cannot check them with BIOVIA Discovery Studio Visualizer, as DS visualizer is not available for OSX, but you can check whether DSV interprets correctly the molecule I used.

I downloaded your molecules first in PDB format and then in pdbqt format as visualized in Discovery Studio. The problem is still the same. Please the images 1 and 2 respectively.

This indicates that the problem lies within the way Discovery Studio interprets the pdbqt files, not in the files themselves.

Thank you very much Annemarie Honegger for your help.