After uploading ligand-protein docked pdb structure and PDB manipulation options, when i click Next step: Generate PDB, it always shows CHARMM was terminated abnormally. Any recommendation how to solve this problem?
Have you separated protein and ligand in .pdb file with TER? If not, the unusual bond might form by the charmm-gui. when you run it system simply explodes.
Jamoliddin Razzokov Sir, i put the ligand-protein dock pdb format in solution builder of charmm gui and tick the heteatom and next is search csml/mol2 to generate pdb. After this the charmm terminated abnormally. Should i separate protein and ligand from protein-ligand docked pdb?