If you have trouble getting a working mol2 file, please contact us. Then convert the mol file into a mol2 file using openbabel. or draw the molecule in 2D in Chemaxon Marvin Sketch (free), add hydrogens, generate 3D coordinates and save the molecule in the "MDL molfile (mol)" format.or use openbabel to convert a correct 3D file from another format into the mol2 format,. Interest, add hydrogen atoms (using the Tools/Structure Editing/AddH menu), and save it as a mol2 file, a ligand), you can use the UCSF chimera visualization software to open the PDB file, remove all molecules except the one of or, if the molecule comes from a PDB file (e.g.get it from the ZINC Database if the molecule is already known,.If one fails, you can try one of the following: Now Add hydrogens will pop-up click OK, then Assign Charges to minimize select. Most of the mol2 files will work, whatever their origin. Go to UCSF Chimera Tools -> Structure Editing -> Build Structure. Please, note that the mol2 files submitted to SwissParam should contain all the hydrogen atoms of the molecule.įirst of all, try the mol2 file you already have. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen).
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