Mercurial > repos > bgruening > openduck_run_smd
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
author | bgruening |
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date | Thu, 16 Apr 2020 08:25:46 -0400 |
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<tool id="openduck_run_smd" name="Run OpenDUck" version="@VERSION@"> <description>steered molecular dynamics runs</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ## to run on GPU set OPENDUCK_GPU_PARAM to something like "--gpu-id 1" cp '$ligand' ./ligand.sdf && duck_prepare_sys -p '$protein' -l ./ligand.sdf -c '$chunk' ## -i is interaction, e.g. A_ASP_156_OD2 -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}' \${OPENDUCK_GPU_PARAM} && mv equil.chk eql.chk && mv complex_system.pickle cs.pickle && duck_smd_runs -i eql.chk -p cs.pickle -n '$num' -l '$mdlen' -d '$start_dist' -v '$vel' \${OPENDUCK_GPU_PARAM} && #if $return_tar: tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz * && #end if get_wqb -l '$ligand' -o '$ligand_wqb' ]]></command> <inputs> <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/> <param argument="chunk" type="data" format='pdb' label="Chunk (in PDB format)" help="PDB file produced by chunk tool."/> <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/> <expand macro="interaction_params" /> <param argument="mdlen" type="float" min="0" value="0.05" label="MD run length (ns)" help="Length of initial MD run (prior to steered molecular dynamics runs)."/> <param argument="start_dist" type="float" min="0" value="2.5" label="Starting distance" help="Initial length of the selected interaction between protein and ligand."/> <param argument="num" type="integer" min="0" value="1" label="Number of SMD runs" help="Number of steered molecular dynamics runs to perform."/> <param argument="vel" type="float" min="0" value="0.00001" label="Velocity" help="Distance (in angstroms) to perturb the system per simulation step in the SMD runs. Decreasing this value will increase simulation time."/> <expand macro="tar_param" /> </inputs> <outputs> <data name="ligand_wqb" format="sdf" label="SD-file with DUck score"/> <expand macro="tar_output" /> </outputs> <tests> <test expect_num_outputs="2"> <param name="protein" value="1n2v_apo.pdb" /> <param name="ligand" value="ligand.mol" /> <param name="chunk" value="protein_out_prot.pdb" /> <param name="chain_sel" value="A" /> <param name="res_sel" value="ASP" /> <param name="resid_sel" value="156" /> <param name="atom_sel" value="OD2" /> <param name="num" value="1" /> <param name="mdlen" value="0.05" /> <param name="start_dist" value="2.5" /> <param name="vel" value="0.00001" /> <output name="ligand_wqb" file="ligand_wqb.mol" lines_diff="2" /> <output name="tar" > <assert_contents> <has_size value="6718500" delta="500"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Perform steered molecular dynamics runs for dynamic undocking (DUck), performing system preparation (topology calculation and minimization), an initial MD run, and SMD runs. This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools. _____ .. class:: infomark **Input** - PDB file for apoprotein - PDB file for chunk - SDF/MOL file for ligand - Parameters defining the protein-ligand interaction - Parameters for MD and SMD runs _____ .. class:: infomark **Output** - Ligand in SDF/MOL format, with added `<SCORE.DUCK_WQB>` parameter. A tar file is also produced as a optional output, containing all files produced by the tool. ]]></help> <expand macro="citations" /> </tool>