Code structure

The main script peptidebuilder.tcl is at the root of the archive. It mainly reads the configuration file, and starts relevant routines for the output, whether it is linked to Espresso or not.

The examples/ folder contains example scripts that can be used to build peptides.

The src/ folder contains all the code. From here we have :

• chain_parameters.tcl - contains geometry information as well as force field.
• espresso/ - all routines that are related to the integration of the script in Espresso. From here will be ran the MD integrator to run a simulation.
• input/ - will build a peptide from a sequence of amino acids. Can also add chemical resolution by appending hydrogen and oxygen atoms.
• mmsg/ - a standard output wrapper. Easier to determine to which part of the code a given message belongs to. This was written by Ira Cooke.
• output/ - creates the VMD-compatible .psf and .pdb files. There is also a vmd_startup file created during the process. But this needs the 'loadseries' command in VMD, which has to be added as a plugin.
• utils/ - contains lots of useful routines. Mainly math-geometry functions that are used to build a peptide.