Installation

Nothing to compile, it's all written in Tcl. Untar the archive in any directory. Set the PEPTIDEB_DIR environment variable to your shell, setting it to its installation path. For example, under bash, extracting the archive in the HOME directory, one should add to ~/.bashrc:

export PEPTIDEB_DIR=~/peptideB

where the executable peptidebuilder.tcl is located inside $PEPTIDEB_DIR. Don't forget to add this folder to your $PATH as well, and source your bash.

• In order for peptideB to be used whithin ESPResSo: Open your espresso configuration file ~/.espressorc (create a new one if necessary) and add the following two lines:

   lappend auto_path "$env(PEPTIDEB_DIR)/src/"
   source $env(ESPRESSO_SCRIPTS)/parallel_tempering.tcl
  

  Also, for the force field to work properly, you should copy the myconfig.h file included in the home directory of peptideB to the home directory of ESPResSo. This will activate all (or almost all!) the necessary features of ESPResSo to run the simulations properly.

• In order to use the 'loadseries' command in VMD, you must source a file to your ~/.vmdrc. To do so, copy the file vmd_plg.tcl located in the vmd_plugin/ directory wherever you want. Then append (or create) the init file ~/.vmdrc by using

   source [VMD_PLUGIN_DIRECTORY]/vmd_plg.tcl
  

  where you should replace [...] by the directory you chose for the vmd_plg.tcl file.

• In order to use secondary structure assignment, you need to compile STRIDE. It is located in peptideb/packages/stride. A simple make in that directory should be enough. Don't forget to add STRIDE to your PATH environment variable. Please see stride/doc/stride/doc for more details.