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.
Experimental data on small molecules
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
Topologies, parameters, and structures for molecular dynamics codes
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
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.)
Tools for force field conversion
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: