Setting up (CHARMM)

Starting from a PDB

For this tutorial, we're going to assume you want to start from a PDB. This can raise some formatting issues, as the PDB format is rarely stuck to exactly, and even the slightest error can cause CHARMM to complain, and fail to read it in. If you have problems, you should compare your PDB file to the one we use here, and make the necessary changes yourself in vi. If you already have a .crd file to use, congratulations! You can safely skip the next section - although you will still need a PDB file to generate a perm.allow for your system automatically.

NOTE: if your system is NOT a standard peptide/protein, you will need to make the perm.allow file manually!

You can download the PDB we're using as the starting point for this tutorial here.

Converting a PDB into CHARMM .crd (CARD) format

In order to run GMIN, OPTIM or PATHSAMPLE using CHARMM, your input must be in CHARMM '.crd' or CARD format. You can do this using scripts form the MMTSB toolset, or just using CHARMM itself.