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To automatically process a ligand, edit the pdb file and change "HETATM" to "LIGAND" in columns 1-6 of the pdb file as shown in the following example. Save the pdb file and process it as you would a regular pdb file.

H++ uses two additional open source software packages for processing the ligand molecules - Open Babel and ANTECHAMBER . Open Babel is used to add H atoms to the ligand. ANTECHAMBER is used to set up the parameters of the ligand to prepare AMBER topology and coordinate files used further in the calculations. Generalized Amber Force Field (GAFF) parameters are used for optimizing the positions of the hydrogens added to the ligand. GAFF includes force field parameters for the organic chemical space beyond the biological molecules coverd by the traditional AMBER force field parameters. The partial atom charges are calculated semi-emperically by AM1-BCC method. If you know the net integer charge of the ligand, it is best to specify it in your pdb input. For example, if the charge is +2, copy and pase the following line someplace at the top of the file: REMARK LIGAND_NET_CHARGE 2 END_LIGAND_INFO. If the explicit net charge info is absent from the input PDB, ANTECHAMBER is first run assuming the ligand molecule has a net charge of 0. If this is found to be inconsistent with the ligand's electronic configuration, ANTECHAMBER is re-run assuming a net charge of +1. IT IS EXTREMELY IMPORTANT TO REALIZE that while this prescription is OK for many compounds, it is NOT always the correct one, even though the calculation may run all the way to the end. Check the master log file for messages that specify the ANTECHAMBER parameters used. If these parameters are not appropriate consider the manual alternative described in the FAQ.

Remember, only one ligand can be processed per run. To try out this capability download this sample pdb file with ligand 2mth_l.pdb or use one of your own.