After you build a periodic box just calculate its volume and then add as many ligand molecules as required to obtain the desired concentration (it's a trivial calculation since you know the molecular mass of the ligand).

Bartosz Trzaskowski can I ask again. How to add many ligands molecules. If Im using CHARMM GUI can I add of many ligand that i want?

Hi, have you solved this problem? would you mind to tell me how to do it? Thank you.

Citra Hasanah sure, if you want to ask me, you can text me by email. This is my email [email protected]