pdb2pqr(1) [debian man page]

PDB2PQR(1)							  PDB2PQR Manual							PDB2PQR(1)

NAME

       pdb2pqr - Generate PQR files for use in electrostatics calculations

SYNOPSIS

       pdb2pqr [--nodebump] [--noopt] [--chain] [--assign-only] [--clean] [--ffout=name] [--with-ph=ph] [--apbs-input] [--ligand=path]
	       [[--verbose] | [-v]] --ff=forcefield path output-path

       pdb2pqr {--help | -h}

DESCRIPTION

       pdb2pqr automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for
       converting protein files in PDB format (path) to PQR format (output-path). These tasks include:

       o   Adding a limited number of missing heavy atoms to biomolecular structures

       o   Determining side-chain pKas

       o   Placing missing hydrogens

       o   Optimizing the protein for favorable hydrogen bonding

       o   Assigning charge and radius parameters from a variety of force fields

OPTIONS

       pdb2pqr accepts the following options:

       --ff=forcefield
	   The forcefield to use. Current values are amber, charm, parse and tyl06.

       --help, -h
	   Print a help message and exit.

       --nodebump
	   Do not perform debumping operation.

       --noopt
	   Do not perform hydrogen optimization.

       --chain
	   Keep the chain ID in the output PQR file.

       --assign-only
	   Only assigns charges to add atoms, debump, or optimize.

       --clean
	   Do no optimization, atom addition, or parameter assignment, just return the original PDB file in alligned format.

       --ffout=name
	   Instead of using the standard caninical naming scheme for residue and atom names, use the names from the given forcefield.

       --with-ph=ph
	   Use propka to calculate pKas and apply them to the molecule given the pH value. Actual PropKa results will be output to
	   output-path.propka.

       --apbs-input
	   Create an APBS input file based on the generated PQR file. Also create a Python pickle for using these parameters in other programs.

       --ligand=path
	   Calculate the parameters for the ligand in MOL2 format at the given path. Pdb2pka must be compiled.

       --verbose, -v
	   Print additional information to screen.

EXTENSIONS

       Extensions add functionality to PDB2PQR and are called by passing a parameter to pdb2pqr. They put their results into files located in
       output-path.

       The following extensions can be used by pdb2pqr:

       --phi
	   Print the per-residue backbone phi angle to output-path.phi.

       --psi
	   Print the per-residue backbone psi angle to output-path.phi.

       --hbond
	   Print a list of hygrogen bonds to output-path.hbond.

       --chi
	   Print the per-residue backbone chi angle to output-path.chi.

       --contact
	   Print a list of contacts to output-path.con.

       --hbondwhatif
	   Print a list of hydrogen bonds to output-path.hbo.

       --salt
	   Print a list of salt bridges to output-path.salt.

       --rama
	   Print the per-residue phi and psi angles to outpath-path.rama.

CITING PDB2PQR
       Please acknowledge your use of pdb2pqr by citing:

       Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann
       electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004).

SEE ALSO

       psize(1)

AUTHOR

       Manuel Prinz <debian@pinguinkiste.de>
	   Wrote this manpage for the Debian System.

COPYRIGHT

       Copyright (C) 2008 Manuel Prinz

pdb2pqr 							    2008-06-04								PDB2PQR(1)

mkdssp(1)							   USER COMMANDS							 mkdssp(1)

NAME

       mkdssp - Calculate secondary structure for proteins in a PDB file

SYNOPSIS

       mkdssp [OPTION] pdbfile [dsspfile]

DESCRIPTION

       The  mkdssp  program  was originally designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment.  DSSP is a
       database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and mkdssp is the appli-
       cation that calculates the DSSP entries from PDB entries.  Please note that mkdssp does not predict secondary structure.

OPTIONS

       If  you	invoke	mkdssp	with only one parameter, it will be interpreted as the PDB file to process and output will be sent to stdout. If a
       second parameter is specified this is interpreted as the name of the DSSP file to create. Both the input and the output file names may have
       either .gz or .bz2 as extension resulting in the proper compression.

       -i, --input filename
	      The file name of a PDB formatted file containing the protein structure data. This file may be a file compressed by gzip or bzip2.

       -o, --output filename
	      The file name of a DSSP file to create. If the filename ends in .gz or .bz2 a compressed file is created.

       -v, --verbose
	      Write out diagnositic information.

       --version
	      Print the version number and exit.

       -h, --help
	      Print the help message and exit.	The directory containing the parser scripts for mrs.

THEORY

       The  DSSP  program works by calculating the most likely secondary structure assignment given the 3D structure of a protein. It does this by
       reading the position of the atoms in a protein (the ATOM records in a PDB file) followed by calculation of the H-bond  energy  between  all
       atoms.  The  best two H-bonds for each atom are then used to determine the most likely class of secondary structure for each residue in the
       protein.

       This means you do need to have a full and valid 3D structure for a protein to be able to calculate the  secondary  structure.   There's	no
       magic in DSSP, so e.g. it cannot guess the secondary structure for a mutated protein for which you don't have the 3D structure.

DSSP FILE FORMAT

       The  header part of each DSSP file is self explaining, it contains some of the information copied over from the PDB file and there are some
       statistics gathered while calculating the secondary structure.

       The second half of the file contains the calculated secondary structure information per residue. What follows is a  brief  explanation  for
       each column.

       Column Name				 Description
       --------------------------------------------------------------------------------------------------------------------------------------------
       #					 The residue number as counted by mkdssp
       RESIDUE					 The residue number as specified by the PDB file followed by a chain iden-
						 tifier.
       AA					 The one letter code for the amino acid. If this letter is lower case this
						 means	this  is a cysteine that form a sulfur bridge with the other amino
						 acid in this column with the same lower case letter.

       STRUCTURE				 This is a complex column containing multiple sub columns.  The first col-
						 umn contains a letter indicating the secondary structure assigned to this
						 residue. Valid values are:
							       Code					  Description
								 H					  Alpha Helix
								 B					  Beta Bridge
								 E					  Strand
								 G					  Helix-3
								 I					  Helix-5
								 T					  Turn
								 S					  Bend
						 What follows are three column indicating for  each  of  the  three  helix
						 types	(3,  4	and 5) whether this residue is a candidate in forming this
						 helix. A > character indicates it starts a helix, a number  indicates	it
						 is inside such a helix and a < character means it ends the helix.
						 The  next  column  contains  a  S character if this residue is a possible
						 bend.
						 Then there's a column indicating the chirality and  this  can	either	be
						 positive  or negative (i.e. the alpha torsion is either positive or nega-
						 tive).
						 The last two columns contain beta bridge labels. Lower  case  here  means
						 parallel bridge and thus upper case means anti parallel.
       BP1 and BP2				 The  first and second bridge pair candidate, this is followed by a letter
						 indicating the sheet.
       ACC					 The accessibility of this residue, this is the surface area expressed	in
						 square Angstrom that can be accessed by a water molecule.
       N-H-->O..O-->H-N 			 Four  columns,  they give for each residue the H-bond energy with another
						 residue where the current residue is either acceptor or donor. Each  col-
						 umn contains two numbers, the first is an offset from the current residue
						 to the partner residue in this H-bond (in  DSSP  numbering),  the  second
						 number is the calculated energy for this H-bond.
       TCO					 The  cosine  of  the  angle between C=O of the current residue and C=O of
						 previous residue. For alpha-helices, TCO is near +1, for beta-sheets  TCO
						 is near -1. Not used for structure definition.
       Kappa					 The virtual bond angle (bend angle) defined by the three C-alpha atoms of
						 the residues current - 2, current and current + 2. Used  to  define  bend
						 (structure code 'S').
       PHI and PSI				 IUPAC peptide backbone torsion angles.
       X-CA, Y-CA and Z-CA			 The C-alpha coordinates

HISTORY

       The original DSSP application was written by Wolfgang Kabsch and Chris Sander in Pascal. This version is a complete rewrite in C++ based on
       the original source code. A few bugs have been fixed since and the algorithms have been tweaked here and there.

TODO

       The code desperately needs an update. The first thing that needs implementing is the improved recognition of pi-helices. A second  improve-
       ment would be to use angle dependent H-bond energy calculation.

BUGS

       If you find any, please let me know.

AUTHOR

       Maarten L. Hekkelman (m.hekkelman (at) cmbi.ru.nl)

version 2.0.4							    18-apr-2012 							 mkdssp(1)