Mercurial > repos > bgruening > autodock_vina_prepare_receptor
changeset 1:8b9b960c9409 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author | bgruening |
---|---|
date | Tue, 07 May 2019 13:32:31 -0400 |
parents | d15e5a2a7558 |
children | 05a13d377b28 |
files | prepare_receptor.xml |
diffstat | 1 files changed, 26 insertions(+), 9 deletions(-) [+] |
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--- a/prepare_receptor.xml Sat Jun 04 12:37:59 2016 -0400 +++ b/prepare_receptor.xml Tue May 07 13:32:31 2019 -0400 @@ -1,5 +1,5 @@ <tool id="prepare_receptor" name="Prepare receptor" version="0.1.0"> - <description>Tool to prepare receptor for Autodock Vina</description> + <description>Tool to prepare receptor for docking with Autodock Vina</description> <requirements> <requirement type="package" version="1.5.6">mgltools</requirement> </requirements> @@ -22,14 +22,23 @@ </test> </tests> <help><![CDATA[ - ** What it does? ** + +.. class:: infomark - This tool uses the MGLTools programming packages to convert a pdb molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking. +**What this tool does** + +This tool uses the MGLTools programming package to convert a pdb file to pdbqt file, which the Autodock Vina program uses to perform molecular docking. The output file has a similar format to the pdb input, with atom type modified to conform to AutoDock atom types and an extra column containing Gasteiger charges added. + +----- - ** input ** +.. class:: infomark + +**Input** - It's required at least one pdb dataset in history, what is informed in ligand field, for use the tool. The pdb molecule file looks like the following example: - +A pdb input file is required. + +* Example:: + ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C @@ -58,9 +67,15 @@ ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C - ** output ** +----- + +.. class:: infomark - The output is a pdbqt molecule file converted from a pdb molecule file. The pdbqt molecule file looks like the following example: +**Output** + +The output is a pdbqt file - effectively the same as a pdb file, but with an extra column containing Gasteiger charges. + +* Example:: ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA @@ -85,7 +100,9 @@ ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD - ]]></help> + + + ]]></help> <citations> <citation type="doi">10.1002/jcc.21334</citation> </citations>