FD/DH pKa calculation code, Warwicker Lab, Manchester 2011 References Warwicker (2004) Protein Science Warwicker (2011) Proteins, submitted The code and data is available as a tar file. The files contained are: for BUILDING the FD/DH code: .f fortran files, should be suitable for compilation on 32 bit or 64 bit machines FDDH_export_build.scr script will build the appropriate binaries - just sub in your compiler for RUNNING FD/DH code: multi_FDDHpK_export.scr scripts goes through the complete process from a list of PDBs to pKs for each PDB FDDHpdb.list the list of PDBs for calculation with the multi_FDDHpK_export.scr script, each PDB (one per line) listed as X.A, mean look for chain A in PDB file X.pdb example PDBs the example FDDHpdb.list links to the two 3BDC derived PDBs supplied .in, .ctr, .chr, .dat files are various standard parameter or dictionary files DIRECTORIES: paths in multi_FDDHpK_export.scr are currently (change as you wish, and move files) set to: ./bin built binaries ./data .in, .ctr, .chr, .data files and the PDB files . program running and pK output files ENVIRONMENT VARIABLES: there are several parameters set by these in multi_FDDHpK_export.scr, including: PROT_DIEL = 10 TARGET_VAL = 1.0 (VdW tolerance for sidechain repacking) I will include more information here, hopefully very soon. jim.warwicker@manchester.ac.uk