I already look in the turorial however that is not the thing that I try to look for. I would like to merge the ligand into the protein and then make the contrain between two atoms, one from the liagand and one from the protein. However, as far as I know, I can do the constraint or restraint just in the one chain. I cant do that with the different chain. So that i try to merge ligand chain and protein chain. I tried to do that with pdb2gmx but it is not work. So that i would like to know is there any way to merge the ligand chain with the protein chain.
Thanks for all your suggstions
Best Regard
Kanin
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