Hi Sebastian,
Since you are using Chimera, I'll use it as a platform to expand on what Thomas said. Thomas said that you have to prepare a lib file and still have the PDB with receptor an complex. Your original file is the complex, in chimera you just need to generate the ligand just by extracting it as you mentioned. You use the ligand only to prepare the lib file. After that you need the complex+lib file to actually obtain both the receptor and ligand for an MD run.
I usually protonate my ligands in Chimera and then save them as mol2 files. That has always worked fine for me.
Best regards.
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Received on Wed Apr 10 2013 - 14:00:32 PDT
