Hi, I have a pdb file containing only one ligand. There is already .gro and .itp files of this ligand at Automated Topology Builder (ATB). I want to use the gro and .itp files of this ligand from ATB. The ligand coordinates in my pdb file is different than at ATB. i.e. ATB have used another coordinates when it obtains .gro and .itp files.
can I use these files obtained from ATB? If ok, doesn't the location/position of the ligand change in the enzyme? Greetings -- Ahmet Yıldırım
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