Resources¶

Ligandbook aims to be a useful resource for the simulation community but by no means is it the only site providing data on small molecules. The sites listed below contain additional resources, such as experimental data for compounds and servers or databases for force field topologies and parameters.

Packages in Ligandbook link compounds to PubChem via the compound ID. Experimental data can the be typically found through PubChem. If a compound is a known ligand in the Protein Databank then its PDB ligandcode is also linked to the ligand summary in the PDB.

Additional resources that might be of interest and are not directly accessible through PubChem or the PDB are listed here (without any claim to be complete).

• Minnesota Solvation Database, a database for experimental solvation free energies for compounds in water and organic solvents.
• LOGKOW, a database of octanol-water coefficents.

If Ligandbook does not contain the parameters or structures that your are looking for then you might be able to find them elsewhere on the Internet. A small and necessarily incomplete selection of resources is listed here.

• Lipidbook is a repository for lipid and detergent parameters for a wide range of force fields and simulation codes. (It is a sister site of Ligandbook, operating under the same principles.)
• ParamChem provides reference data organizers and generators as well as workflows for automatic parameterization of Molecular Mechanics (MM) Force Fields as well as Semi-Empirical (SE) methods (geared towards the CHARMM force field). In particular, it allows generation of topologies with the CGenFF (the CHARMM General Force Field for organic molecules).
• Antechamber is a tool that allows the generation of AMBER topologies with GAFF, the General AMBER Force Field.
• The Automated Topology Builder (ATB) and Repository contains GROMOS96 force field parameters for many small molecules.
• Virtual Chemistry Database contains parameters (OPLS-AA, AMBER/GAFF and CHARMM/CGenFF formatted for Gromacs) and validation data for more than 3000 organic molecules.
• SwissParam generates topologies for Gromacs and CHARMM for small organic molecules, based on the Merck Molecular ForceField (MMFF) and CHARMM22. These parameters are primarily intended for drug design type calculations but they can also be used as starting parameters for more detailed parameterization efforts as required for normal mode calculations or molecular dynamics simulations. (See also the SwissParam tutorial for Gromacs.)

If necessary, the coordinate and topology files available in Ligandbook can be converted into or from other commonly used file formats (AMBER, CHARMM, Desmond, LAMMPS, etc.) using some of the following open source tools:

• InterMol
• ParmEd
• ACPYPE (Google Code archive; see also ACPYPE in the CCPN SVN repository)