pdb2pqr

port 可以安裝囉

sh-3.2# port install pdb2pqr
--->  Computing dependencies for pdb2pqr
--->  Fetching archive for pdb2pqr
--->  Attempting to fetch pdb2pqr-1.7_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/pdb2pqr
--->  Fetching distfiles for pdb2pqr
--->  Attempting to fetch pdb2pqr-1.7.tar.gz from http://nchc.dl.sourceforge.net/pdb2pqr
--->  Verifying checksum(s) for pdb2pqr
--->  Extracting pdb2pqr
--->  Configuring pdb2pqr
--->  Building pdb2pqr
--->  Staging pdb2pqr into destroot
--->  Installing pdb2pqr @1.7_0
--->  Activating pdb2pqr @1.7_0
--->  Cleaning pdb2pqr
--->  Updating database of binaries: 100.0%
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.



Command line

sh-3.2# pdb2pqr
Incorrect number (0) of arguments!
argv: ['/opt/local/share/pdb2pqr/pdb2pqr.py'], args: []
pdb2pqr  (Version 1.7)

This module takes a PDB file as input and performs
optimizations before yielding a new PDB-style file as
output

Usage: pdb2pqr.py [options] --ff=
    Required Arguments:
          :  The forcefield to use - currently amber,
                         charmm, parse, tyl06, peoepb and swanson
                         are supported.
                :  The path to the PDB file or an ID
                         to obtain from the PDB archive
        :  The desired output name of the PQR file
                         to be generated
    Optional Arguments:
        --nodebump    :  Do not perform the debumping operation
        --noopt       :  Do not perform hydrogen optimization
        --chain       :  Keep the chain ID in the output PQR file
        --assign-only :  Only assign charges and radii - do not add
                         atoms, debump, or optimize.
        --clean       :  Do no optimization, atom addition, or
                         parameter assignment, just return the
                         original PDB file in aligned format.
        --ffout=:  Instead of using the standard canonical
                         naming scheme for residue and atom names,
                         use the names from the given forcefield.
        --with-ph=:  Use propka to calculate pKas and apply them
                         to the molecule given the pH value. Actual
                         PropKa results will be output to
                         .propka.
        --apbs-input  :  Create a template APBS input file based on
                         the generated PQR file.  Also creates a Python
                         pickle for using these parameters in other programs.
        --ligand=: Calculate the parameters for the ligand in
                         mol2 format at the given path. Pdb2pka must
                         be compiled
        --whitespace  :  Insert whitespaces between atom name and residue
                         name, between x and y, and between y and z
        --typemap :      Create Typemap output
        --neutraln  :    Make the N-terminus of this protein neutral
                         (default is charged)
        --neutralc  :    Make the C-terminus of this protein neutral
                         (default is charged)
        --verbose (-v):  Print information to stdout
        --help    (-h):  Display the usage information

    Optional Arguments from Extensions Directory:
        --phi         :  Print the per-residue backbone phi
                         angle to {output-path}.phi
        --hbondwhatif :  Print a list of hydrogen bonds to
                         {output-path}.hbo
        --hbond       :  Print a list of hydrogen bonds to
                         {output-path}.hbond
        --chi         :  Print the per-residue backbone chi
                         angle to {output-path}.chi
        --psi         :  Print the per-residue backbone psi
                         angle to {output-path}.psi
        --contact     :  Print a list of contacts to
                         {output-path}.con
        --salt        :  Print a list of salt bridges to
                         {output-path}.salt
        --rama        :  Print the per-residue phi and psi
                         angles to {output-path}.rama for
                         Ramachandran plots