Getting started with Ligandbook
Ligandbook helps you to find other people's forcefield parameters
and to disseminate your own parameter sets. The following
sections tell you how to do this.
How to find force field parameters for a compound
Ligandbook stores forcefield parameters in
packages. For a given molecule,
a package contains the 3D structure of the compound (in PDB format) and the
topology together with atom types and partial charges
(e.g. for the Gromacs simulation code, a single itp file).
For each molecule, extensive metadata such as alternative names, molecular weight,
total charge, and the chemical structure are stored. Therefore, there exist two different
ways to search the database for a compound:
- text search on the metadata (using the
search box at the top left on each page)
- structure search on
chemical (sub)structures (using Ligandbook's
Sketcher chemical drawing application)
For text search one can use boolean expressions
and wildcards. The substructure search
allows you to chemically draw the query molecule (or a characteristic part of it). The search
then returns all molecules from the database that contain the drawn structure. (It is also
possible to provide the search structure as a SMILES
If appropriate packages were found then you should look at them individually.
Check that the compound is the correct stereoisomer; read any referenced papers;
download the parameter files and look at them yourself. Ligandbook only helps you to find
parameter sets but you are responsible for judging if they are appropriate for your work,
how you use them, and how far you trust them to be accurate.
When you use parameters downloaded from Ligandbook in published work then you
must cite any publications that are referenced with the parameters (see the file
citation.txt that is included in the download).
How to submit a new package
You have parameterized a new compound or validated a set of parameters that you generated
through some other means. You published a paper in which your report the parameters, the validation
and perhaps also an application. You would like to share the results with the community and
also make sure that anyone using your parameters gives credit where credit is due and cites
You decide that you will put the parameters on Ligandbook; because your parameter are
linked to your citation and distributed together, it will be easy for anyone else using
your work to also cite you.
In the following we assume that you have your parameters in a format suitable for
the Gromacs package and you
use an all-atom forcefield such as OPLS-AA (these are currently the best supported
- The required input files are
file containing the coordinates and an itp file containing the force field parameters
and topology. (For other MD codes, the itp file is replaced by a corresponding topology file.)
- You must be logged into Ligandbook in order to upload a new package. You can freely register by
going to the registration page and following the steps described there.
Once you have completed the registration process (by clicking on the activation link received by email),
log in into the site
- Go to the new package form, by clicking on the Deposit link at the top of the page.
The form opens on a new page. Note that fields marked with
* are compulsory.
- Choose the software (code) and force field for which the input files were generated,
and fill in the abstract in which you should describe how these parameters were generated, some specific
details related to their use, etc.
- For the license, fill in the name and the email
of the license owner (it may be different from you),
the source of these files and choose the type of license (CC0,
CC BY-SA or CC BY-NC-SA)
that is most appropriate. Note that you must be the copyright owner of the parameters (e.g. by virtue of
having created them) or must have obtained them under a licence that permits you to select one of the licences available
- Select the input .pdb and .itp files on your local disk. These fields will be uploaded and provided as they are,
with the only exception that the residue name will be changed to the 3-letter ligand code, which is determined
automatically during the upload process).
- When everything is ready, click on the Create button.
- In the next step, your files are analyzed and you will be prompted to verify if the compound structure,
as it was interpreted from the .pdb file, is in agreement with what you are expecting.
- If this is the case, click on the button Approve, chemical structure is correct and
your submission is complete.
- If not, click on the Fix, chemical structure is wrong button and you will be
redirected to a molecular drawer, where you can draw the correct structure.
Once you are done, click on the Apply corrections button.
Ligandbook will show you again how it interprets your input. Once you are
satisfied click Approve, chemical structure is correct.
- Add one or more references which are pertinent for these force field parameters;
if the reference can be found on PubMed then it is sufficient to simply fill in the PubMedID and the remaining bibliographical information is automatically fetched.
Metadata such as abstract and citations can be changed and updated any time once a parameter package
has been created. Parameters themselves, on the other hand, can not be replaced. Instead, a new
version is automatically created. In this way, the history of the parameter development is