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.

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 string.)

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).

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 your paper.

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 formats).

• The required input files are PDB format 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

1. 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.
2. 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.
3. 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 here.
4. 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).
5. When everything is ready, click on the Create button.
6. 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.
   1. If this is the case, click on the button Approve, chemical structure is correct and your submission is complete.
   2. 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.
7. 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 conserved.