Mercurial > repos > bgruening > openduck_run_smd
comparison openduck_run_smd.xml @ 0:05c95b16823b draft default tip
"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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-1:000000000000 | 0:05c95b16823b |
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1 <tool id="openduck_run_smd" name="Run OpenDUck" version="@VERSION@"> | |
2 <description>steered molecular dynamics runs</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 ## to run on GPU set OPENDUCK_GPU_PARAM to something like "--gpu-id 1" | |
9 cp '$ligand' ./ligand.sdf && | |
10 | |
11 duck_prepare_sys | |
12 -p '$protein' | |
13 -l ./ligand.sdf | |
14 -c '$chunk' | |
15 ## -i is interaction, e.g. A_ASP_156_OD2 | |
16 -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}' | |
17 \${OPENDUCK_GPU_PARAM} && | |
18 | |
19 mv equil.chk eql.chk && | |
20 mv complex_system.pickle cs.pickle && | |
21 | |
22 duck_smd_runs | |
23 -i eql.chk | |
24 -p cs.pickle | |
25 -n '$num' | |
26 -l '$mdlen' | |
27 -d '$start_dist' | |
28 -v '$vel' | |
29 \${OPENDUCK_GPU_PARAM} && | |
30 #if $return_tar: | |
31 tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz * && | |
32 #end if | |
33 get_wqb -l '$ligand' -o '$ligand_wqb' | |
34 ]]></command> | |
35 <inputs> | |
36 <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/> | |
37 <param argument="chunk" type="data" format='pdb' label="Chunk (in PDB format)" help="PDB file produced by chunk tool."/> | |
38 <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/> | |
39 <expand macro="interaction_params" /> | |
40 <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)."/> | |
41 <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."/> | |
42 <param argument="num" type="integer" min="0" value="1" label="Number of SMD runs" help="Number of steered molecular dynamics runs to perform."/> | |
43 <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."/> | |
44 <expand macro="tar_param" /> | |
45 </inputs> | |
46 <outputs> | |
47 <data name="ligand_wqb" format="sdf" label="SD-file with DUck score"/> | |
48 <expand macro="tar_output" /> | |
49 </outputs> | |
50 <tests> | |
51 <test expect_num_outputs="2"> | |
52 <param name="protein" value="1n2v_apo.pdb" /> | |
53 <param name="ligand" value="ligand.mol" /> | |
54 <param name="chunk" value="protein_out_prot.pdb" /> | |
55 <param name="chain_sel" value="A" /> | |
56 <param name="res_sel" value="ASP" /> | |
57 <param name="resid_sel" value="156" /> | |
58 <param name="atom_sel" value="OD2" /> | |
59 <param name="num" value="1" /> | |
60 <param name="mdlen" value="0.05" /> | |
61 <param name="start_dist" value="2.5" /> | |
62 <param name="vel" value="0.00001" /> | |
63 <output name="ligand_wqb" file="ligand_wqb.mol" lines_diff="2" /> | |
64 <output name="tar" > | |
65 <assert_contents> | |
66 <has_size value="6718500" delta="500"/> | |
67 </assert_contents> | |
68 </output> | |
69 </test> | |
70 </tests> | |
71 <help><![CDATA[ | |
72 | |
73 .. class:: infomark | |
74 | |
75 **What it does** | |
76 | |
77 Perform steered molecular dynamics runs for dynamic undocking (DUck), performing system preparation (topology calculation and minimization), an initial MD run, and SMD runs. | |
78 | |
79 This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools. | |
80 | |
81 _____ | |
82 | |
83 .. class:: infomark | |
84 | |
85 **Input** | |
86 | |
87 - PDB file for apoprotein | |
88 - PDB file for chunk | |
89 - SDF/MOL file for ligand | |
90 - Parameters defining the protein-ligand interaction | |
91 - Parameters for MD and SMD runs | |
92 | |
93 _____ | |
94 | |
95 | |
96 .. class:: infomark | |
97 | |
98 **Output** | |
99 | |
100 - Ligand in SDF/MOL format, with added `<SCORE.DUCK_WQB>` parameter. | |
101 | |
102 A tar file is also produced as a optional output, containing all files produced by the tool. | |
103 | |
104 ]]></help> | |
105 | |
106 <expand macro="citations" /> | |
107 </tool> |