newhyd - inserts protons into a PDB heavy atom file SYNOPSIS newhyd DESCRIPTION newhyd takes a PDB file and attaches protons according to hybridization and connectivity information contained in a pair of database files. Protons are given rational four- character names according to the rules: Carbon protons are named H/remoteness/branch/sequence: CA, CB, CG1 -> HA, HB1, HB2, HG11, HG12 Heteroatom protons are H/hetatm/remote/sequence: NA, NB -> HNA, HNB1, HNB2 or if necessary: H/hetatm/branch/sequence: NH1 -> HN11, HN12 The program queries the user if all protons are to be gen- erated, or if only nonexchangeable protons are wanted. Then it prompts the user for the input file name, output file name, and whether the default database files are to be used for connectivities and hybridization. The user can specify alternate radii and hybrid files which should follow the format of the standard database files. The hybrid database currently contains information for 20 standard amino acids, the nucleic acids ADE, CYT, GUA, THY and URA. Additional residues can be added to the hybridization and connectivity database files if of general utility. INPUT newhyd prompts for four files: Input file name:file.PDB Output file name:fileH.pdb Radii file:(the default can be accepted with a
.) Hybridization file:(the default can be accepted with a .) You can specify your own radii and hybridization files which should follow the format of the athyd.data and chem.con files. FILES athyd.data standard hybridization file chem.con standard radii file AUTHOR newhyd is a modification by Brandan Borgias of N. Pattabiraman's program newfixhy, for generation of hydrogen coordinates from a PDB format coordinate file. Rational names are generated for the protons. Connectivity informa- tion is now generated in the program rather than being required as a seperate previous step. Brandan A. Borgias Department of Pharmaceutical Chemistry University of California--San Francisco BUGS newhyd expects a file with only heavy atoms. It will not strip away protons already in place and will not overwrite protons already present. Limited to 2000 atoms and 400 resi- dues. newhyd expects the N terminal Nitrogen atom to be first in the list and will always protonate it with three protons in sp3 configuration. If N is not atom 1, then it will be given two protons n sp2 configuration. Users wishing neu- tral N-termini must delete the proton of their choice.