Page BornRadii

This pages list the necessary steps to calculate ”perfect” GB radii for a structure given as PDB

• generate a PQR file for the structure (using Charmm Parameter and a pH of 7.0)

  /home/cocktail/held/progs/pdb2pqr-1.2.1/pdb2pqr.py --ff=charmm --with-ph=7.0 <PDB_File> <PQR_File>

• generate an APBS input file for the runGB.py script

  java -cp .:/home/cocktail/held/workspace/MolToolsExtract/bin:/home/cocktail/conrad/work/phd/libs/commons-net/commons-net.jar:/home/cocktail/conrad/work/phd/PROTEOMICS_WORKER/PROTEOMICSWORKER_BASE/classes/:/home/cocktail/held/libs/msbase.jar:/home/cocktail/held/libs/mssqlserver.jar:/home/cocktail/held/libs/msutil.jar:/home/cocktail/held/libs/ganymed-ssh2-build209.jar:/home/cocktail/held/libs/log4j-1.2.13.jar:/home/cocktail/held/libs/sqljdbc.jar:/home/cocktail/held/libs/colt.jar:/home/cocktail/conrad/work/phd/libs/ftp:/home/cocktail/held/libs/moltools.jar:/home/cocktail/noe/java/libraries/metamacs.jar:/home/cocktail/noe/java/libraries/mantissa/mantissa-5.8.jar:/home/cocktail/held/libs/commons-io-1.3.1/commons-io-1.3.1.jar:/home/cocktail/held/libs/Jmol.jar:/home/cocktail/held/workspace/MolGlue/bin/ CreateBornRadiiInput -s <PQR_File> -o <APBS_input_file>
  

• run the runGB_mod.py script to calculate radii

  python /home/cocktail/held/progs/apbs-0.5.1-self/tools/python/runGB_mod.py -i <APBS_input_file>  -o <output_radii_file>