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<appConfig xmlns="http://nbcr.sdsc.edu/opal/types"
xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<metadata appName="PDB2PQR 2.0.0">
<usage><![CDATA[PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. Version 1.9.0.
<BR><A HREF=http://www.nbcr.net/ws_help/PDB2PQR/>
Tutorial: http://www.nbcr.net/ws_help/PDB2PQR/
</A>
]]></usage>
<info xsd:type="xsd:string">
<![CDATA[
pdb2pqr (Version 2.0.0)
Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH
This module takes a PDB file as input and performs optimizations before
yielding a new PQR-style file in PQR_OUTPUT_PATH. If PDB_PATH is an ID it will
automatically be obtained from the PDB archive.
Options:
--version show program's version number and exit
-h, --help show this help message and exit
Manditory options:
One of the following options must be used.
--ff=FIELD_NAME The forcefield to use - currently amber, charmm,
parse, tyl06, peoepb and swanson are supported.
--userff=USER_FIELD_FILE
The user created forcefield file to use. Requires
--usernames overrides --ff
--clean Do no optimization, atom addition, or parameter
assignment, just return the original PDB file in
aligned format. Overrides --ff and --userff
General options:
--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.
--ffout=FIELD_NAME Instead of using the standard canonical naming scheme
for residue and atom names, use the names from the
given forcefield - currently amber, charmm, parse,
tyl06, peoepb and swanson are supported.
--usernames=USER_NAME_FILE
The user created names file to use. Required if using
--userff
--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=PATH 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). Requires PARSE force field.
--neutralc Make the C-terminus of this protein neutral (default
is charged). Requires PARSE force field.
-v, --verbose Print information to stdout.
--drop-water Drop waters before processing protein. Currently
recognized and deleted are the following water types:
HOH, WAT
--include-header Include pdb header in pqr file. WARNING: The resulting
PQR file will not work with APBS versions prior to 1.5
pH options:
--ph-calc-method=PH_METHOD
Method used to calculate ph values. If a pH
calculation method is selected, for each titratable
residue pH values will be calculated and the residue
potentially modified after comparison with the pH
value supplied by --with_ph propka - Use PROPKA to
calculate pH values. Actual PROPKA results will be
output to <output-path>.propka. pdb2pka - Use PDB2PKA
to calculate pH values. Requires the use of the PARSE
force field. Warning: Larger residues can take a very
long time to run using this method. EXPERIMENTAL!
--with-ph=PH pH values to use when applying the results of the
selected pH calculation method. Defaults to 7.0
Extension options:
--chi Print the per-residue backbone chi angle to {output-
path}.chi
--summary Print protein summary information to {output-
path}.summary.
--contact Print a list of contacts to {output-path}.con
--newresinter Print interaction energy between each residue pair in
the protein to {output-path}.newresinter.
--salt Print a list of salt bridges to {output-path}.salt
Hbond extension options:
--hbond Print a list of hydrogen bonds to {output-path}.hbond
--whatif Change hbond output to WHAT-IF format.
--angle_cutoff=ANGLE_CUTOFF
Angle cutoff to use when creating hbond data (default
30.0)
--distance_cutoff=DISTANCE_CUTOFF
Distance cutoff to use when creating hbond data
(default 3.4)
--old_distance_method
Use distance from donor hydrogen to acceptor to
calculate distance used with --distance_cutoff.
Resinter extension options:
--resinter Print interaction energy between each residue pair in
the protein to {output-path}.resinter.
--residue_combinations
Remap residues to different titration states and rerun
resinter appending output. Consider only the minimum
number of whole protein titration combinations needed
to test each possible pairing of residue titration
states. Normally used with --noopt. If a protein
titration state combination results in a pair of
residue being re-tested in the same individual
titration states a warning will be generated if the
re-tested result is different. This warning should not
be possible if used with --noopt.
--all_residue_combinations
Remap residues to ALL possible titration state
combinations and rerun resinter appending output.
Results with --noopt should be the same as
--residue_combinations. Runs considerably slower than
--residue_combinations and generates the same type of
warnings. Use without --noopt to discover how
hydrogen optimization affects residue interaction
energies via the warnings in the output.
Rama extension options:
--rama Print the per-residue phi and psi angles to {output-
path}.rama for Ramachandran plots
--phi_only Only include phi angles in output. Rename output file
{output-path}.phi
--psi_only Only include psi angles in output. Rename output file
{output-path}.psi
]]>
</info>
<types>
<!-- list of flags -->
<flags>
<flag>
<id>verbose</id>
<tag>--verbose</tag>
<textDesc>Print information to stdout</textDesc>
<default>true</default>
</flag>
<flag>
<id>nodebump</id>
<tag>--nodebump</tag>
<textDesc>Do not perform the debumping operation</textDesc>
</flag>
<flag>
<id>noopt</id>
<tag>--noopt</tag>
<textDesc>Do not perform hydrogen optimization</textDesc>
</flag>
<flag>
<id>chain</id>
<tag>--chain</tag>
<textDesc>Keep the chain ID in the output PQR file</textDesc>
</flag>
<flag>
<id>assign-only</id>
<tag>--assign-only</tag>
<textDesc>Only assign charges and radii - do not add atoms, debump, or optimize</textDesc>
</flag>
<flag>
<id>clean</id>
<tag>--clean</tag>
<textDesc>Do no optimization, atom addition, or parameter assignment, just return the original PDB file in aligned format. Overwrites chosen forcefield.</textDesc>
</flag>
<flag>
<id>apbs-input</id>
<tag>--apbs-input</tag>
<textDesc>Create a template APBS input file based on the generated PQR file.
Also creates a Python pickle for using these parameters in other programs.
</textDesc>
</flag>
<flag>
<id>whitespace</id>
<tag>--whitespace</tag>
<textDesc>Insert whitespaces between atom name and residue name,
between x and y, and between y and z </textDesc>
</flag>
<flag>
<id>typemap</id>
<tag>--typemap</tag>
<textDesc>Create Typemap output </textDesc>
</flag>
<flag>
<id>neutraln</id>
<tag>--neutraln</tag>
<textDesc>Make the N-terminus of this protein neutral (default is charged)</textDesc>
</flag>
<flag>
<id>neutralc</id>
<tag>--neutralc</tag>
<textDesc>Make the C-terminus of this protein neutral (default is charged)</textDesc>
</flag>
<flag>
<id>chi</id>
<tag>--chi</tag>
<textDesc>Print the per-residue backbone chi angle to {output-path}.chi</textDesc>
</flag>
<flag>
<id>rama</id>
<tag>--rama</tag>
<textDesc>Print the per-residue phi and psi angles to {output-path}.rama for Ramachandran plots</textDesc>
</flag>
<flag>
` <id>psi_only</id>
<tag>--psi_only</tag>
<textDesc>Only include phi angles in Rama output. Rename output file {output-path}.psi</textDesc>
</flag>
<flag>
<id>phi_only</id>
<tag>--phi_only</tag>
<textDesc>Only include phi angles in Rama output. Rename output file {output-path}.phi</textDesc>
</flag>
<flag>
` <id>contact</id>
<tag>--contact</tag>
<textDesc>Print a list of contacts to {output-path}.con</textDesc>
</flag>
<flag>
` <id>salt</id>
<tag>--salt</tag>
<textDesc>Print a list of salt bridges to {output-path}.salt </textDesc>
</flag>
<flag>
` <id>summary</id>
<tag>--summary</tag>
<textDesc>Print protein summary information to {output-path}.summary.</textDesc>
</flag>
<flag>
<id>hbond</id>
<tag>--hbond</tag>
<textDesc>Print a list of hydrogen bonds to {output-path}.hbond</textDesc>
</flag>
<flag>
<id>whatif</id>
<tag>--whatif</tag>
<textDesc>Change hbond output to WHAT-IF format.</textDesc>
</flag>
<flag>
<id>old_distance_method</id>
<tag>--old_distance_method</tag>
<textDesc>Use distance from donor hydrogen to acceptor to calculate distance used with --distance_cutoff.</textDesc>
</flag>
<flag>
<id>resinter</id>
<tag>--resinter</tag>
<textDesc>Print interaction energy between each residue pair in
the protein to {output-path}.resinter.</textDesc>
</flag>
<flag>
<id>residue_combinations</id>
<tag>--residue_combinations</tag>
<textDesc>Remap residues to different titration states and rerun
resinter appending output. Consider only the minimum
number of whole protein titration combinations needed
to test each possible pairing of residue titration
states. Normally used with --noopt. If a protein
titration state combination results in a pair of
residue being re-tested in the same individual
titration states a warning will be generated if the
re-tested result is different. This warning should not
be possible if used with --noopt.</textDesc>
</flag>
<flag>
<id>all_residue_combinations</id>
<tag>--all_residue_combinations</tag>
<textDesc>Remap residues to ALL possible titration state
combinations and rerun resinter appending output.
Results with --noopt should be the same as
--residue_combinations. Runs considerably slower than
--residue_combinations and generates the same type of
warnings. Use without --noopt to discover how
hydrogen optimization affects residue interaction
energies via the warnings in the output.</textDesc>
</flag>
</flags>
<!-- list of tagged parameters -->
<taggedParams>
<separator>=</separator>
<param>
<id>forcefield</id>
<tag>--ff</tag>
<paramType>STRING</paramType>
<required>true</required>
<value>AMBER</value>
<value>CHARMM</value>
<value>PARSE</value>
<value>PEOEPB</value>
<value>SWANSON</value>
<value>TYL06</value>
<default>PARSE</default>
<textDesc>Currently supported</textDesc>
</param>
<param>
<id>user-forcefield</id>
<tag>--userff</tag>
<paramType>FILE</paramType>
<ioType>INPUT</ioType>
<required>false</required>
<textDesc>User-defined forcefield </textDesc>
</param>
<param>
<id>usernames</id>
<tag>--usernames</tag>
<paramType>FILE</paramType>
<ioType>INPUT</ioType>
<required>false</required>
<textDesc>The user-created names file to use. Required if using user defined forcefield </textDesc>
</param>
<param>
<id>ffout</id>
<tag>--ffout</tag>
<paramType>STRING</paramType>
<value>AMBER</value>
<value>CHARMM</value>
<value>PARSE</value>
<value>PEOEPB</value>
<value>SWANSON</value>
<value>TYL06</value>
<textDesc>Instead of using the standard canonical naming scheme for residue and atom, use names from the given forcefield:</textDesc>
</param>
<param>
<id>ph-calc-method</id>
<tag>--ph-calc-method</tag>
<paramType>STRING</paramType>
<value>PROPKA</value>
<value>PDB2PKA</value>
<required>false</required>
<textDesc>Method used to calculate ph values, if any. If a pH
calculation method is selected, for each titratable
residue pH values will be calculated and the residue
potentially modified after comparison with the pH
value supplied by --with_ph propka - Use PROPKA to
calculate pH values. Actual PROPKA results will be
output to output-path.propka. pdb2pka - Use PDB2PKA
to calculate pH values. Requires the use of the PARSE
force field. Warning: Larger residues can take a very
long time to run using this method. EXPERIMENTAL!</textDesc>
</param>
<param>
<id>with-ph</id>
<tag>--with-ph</tag>
<paramType>FLOAT</paramType>
<required>false</required>
<default>7.0</default>
<textDesc>pH values to use when applying the results of the
selected pH calculation method. Defaults to 7.0</textDesc>
</param>
<param>
<id>ligand</id>
<tag>--ligand</tag>
<paramType>FILE</paramType>
<ioType>OUTPUT</ioType>
<textDesc>Calculate the parameters for the ligand in mol2 format at the given path. Pdb2pka must be compiled.</textDesc>
</param>
<param>
<id>angle_cutoff</id>
<tag>--angle_cutoff</tag>
<paramType>FLOAT</paramType>
<textDesc>Angle cutoff to use when creating hbond data (default 30.0)</textDesc>
</param>
<param>
<id>distance_cutoff</id>
<tag>--distance_cutoff</tag>
<paramType>FLOAT</paramType>
<textDesc>Distance cutoff to use when creating hbond data (default 3.4)</textDesc>
</param>
</taggedParams>
<!-- list of untagged parameters, in order -->
<untaggedParams>
<param>
<id>inId</id>
<paramType>STRING</paramType>
<ioType>INPUT</ioType>
<!-- <required>true</required> -->
<textDesc>a PDB ID (fetch input file from PDB archive; for test use 1a1p)</textDesc>
</param>
<param>
<id>inFile</id>
<paramType>FILE</paramType>
<ioType>INPUT</ioType>
<!-- <required>true</required> -->
<textDesc><![CDATA[ upload a PDB input file (test file <a href="http://www.rcsb.org/pdb/files/1a1p.pdb">http://www.rcsb.org/pdb/files/1a1p.pdb</a>)]]></textDesc>
</param>
<param>
<id>output-file</id>
<paramType>FILE</paramType>
<ioType>OUTPUT</ioType>
<required>true</required>
<default>output.pqr</default>
<textDesc>The desired output name of the PQR file to be generated</textDesc>
</param>
</untaggedParams>
<groups>
<group>
<name>inputParam</name>
<elements>inId inFile</elements>
<required>true</required>
<exclusive>true</exclusive>
<textDesc>Please enter either:</textDesc>
</group>
<group>
<name>ForceFieldGroup</name>
<elements>forcefield </elements>
<required>true</required>
<textDesc>Pick a forcefield to use:</textDesc>
</group>
<group>
<name>UserForceFieldGroup</name>
<elements>user-forcefield usernames</elements>
<required>true</required>
<textDesc>User forcefield to use (overwrites previous forcefield):</textDesc>
</group>
<group>
<name>outputFile</name>
<elements>output-file</elements>
<required>true</required>
<textDesc>Output file name</textDesc>
</group>
<group>
<name>ffoutGroup</name>
<elements>ffout</elements>
<required>false</required>
<textDesc>Pick an output naming scheme to use</textDesc>
</group>
<group>
<name>AvailableOptionsGroup</name>
<elements>clean nodebump noopt chain assign-only ph-calc-method with-ph apbs-input
ligand whitespace typemap neutraln neutralc verbose </elements>
<required>false</required>
<textDesc>Available options </textDesc>
</group>
<group>
<name>ExtensionOptionsGroup</name>
<elements>chi contact salt summary </elements>
<textDesc>Extensions options:</textDesc>
</group>
<group>
<name>HbondExtensionOptionsGroup</name>
<elements>hbond whatif angle_cutoff distance_cutoff old_distance_method </elements>
<textDesc> Hbond Extensions options:</textDesc>
</group>
<group>
<name>ResinterExtensionOptionsGroup</name>
<elements>resinter residue_combinations all_residue_combinations </elements>
<textDesc>Resinter Extensions options:</textDesc>
</group>
<group>
<name>RamaExtensionOptionsGroup</name>
<elements>rama phi_only psi_only </elements>
<textDesc>Rama Extensions options:</textDesc>
</group>
</groups>
</types>
</metadata>
<binaryLocation>/share/apps/pdb2pqr/pdb2pqr.py</binaryLocation>
<drmaaQueue>si</drmaaQueue>
<parallel>false</parallel>
</appConfig>
|
