The MATCH web server allows one to submit a molecule to generate both the topology and parameter file for a given small molecule. Molecule file formats: pdb, sdf, mol, mol2 are all accepted. Keep in mind that regardless of which file format you submit you will be given a pdb in CHARMM compatible format so the initial file format is only used to determine the 3d structure and connectivity of a given molecule. Make sure that all hydrogens are included and everything is in the correct protonation state!
If this is not done the atomic charges will be incorrect.
Upon submitting a molecule, one will be redirected to another page where it is possible to download a tar file that contains the topology (.rtf), parameter file (.prm) and a pdb file in charmm compatible format. If it was not possible to completely parameterize a given molecule an error will be displayed, please consult the MATCH user guide for possible fixes, downloading the full program and source code is also recommended as using the web server has limited functionality.
Valid file extensions: pdb, sdf, mol, mol2