CHARMM-GUI
CHARMM-GUI is a user interface for CHARMM that can be used to easily create CHARMM readable files (which can then be converted to LAMMPS files using charmm2lammps). It is particularly helpful for those unfamiliar with using CHARMM but who need to create CHARMM files. It's pretty simple, but this page includes some information on what features have been useful for the group in the past.
To use CHARMM-GUI for input creation, click on the link for the Input Generator either at the top or left of the main page. Then select the PDB reader on the left sidebar.
The first page will allow you to either upload a PDB file from your computer or download one from the Protein Data Bank. Both options can be useful.
The next page allows you to select which atom groups you want to select. You can easily choose only protein atoms this way (which is usually what you'll want to do).
The next page gives you options for manipulating your PDB. There are quite a few here, but the ones that have been most relevant for the group in the past are:
- Terminal Group Patching: You'll almost always want to choose this one to handle the N- and C-termini properly.
- Model Missing Residues: This will add in any residues missing from the PDB file. This can be helpful if your PDB is missing some residues at the end or anywhere in the protein really.
- Mutation: Can substitute any amino acid in the protein for any other natural amino acid.
- Unnatural Amino Acid Substitution: Can substitute any amino acid in the protein for an unnatural amino acid. Unfortunately, the uAAs that we commonly used are not available in CHARMM-GUI. Refer to the all-atom PEGylation page in the Lab Notebook for information on including uAAs with KPrep.
After choosing your options, going to the next page will produce PDB, CRD, and PSF files that you can download.