Mercurial > repos > chemteam > parmconv

annotate parmconv.xml @ 1:da2252f1ccab draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
author chemteam
date Mon, 25 Jan 2021 11:15:06 +0000
parents 6c6cecf51bd0
children 2b82fc7bec67
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da2252f1ccab "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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1 <tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
0
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2 <description>to AMBER prmtop in preparation for MMPBSA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
0
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.2.0">parmed</requirement>
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9 <requirement type="package" version="2020.4">gromacs</requirement>
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10 <requirement type="package" version="2.11.2">jinja2</requirement>
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11 </expand>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14 python '$templating_script' '$inputs' &&
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15 PATH_TO_PARMED=\$(dirname `which parmed`) &&
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16 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) &&
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17 export GMXDATA=\$AMBERHOME/share/gromacs/top/ &&
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18 parmed -i ligand.script -O &&
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19 parmed -i receptor.script -O &&
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20 parmed -i complex.script -O &&
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21 parmed -i solvatedcomplex.script -O
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23 ]]>
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24 </command>
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25 <configfiles>
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26 <inputs name="inputs"/>
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27 <configfile name="templating_script">
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28 <![CDATA[
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29
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30 import os
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31 import sys
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32 import json
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33
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34 from jinja2 import Environment, FileSystemLoader
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35 input_json_path = sys.argv[1]
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36 params = json.load(open(input_json_path, "r"))
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37 currentpath = "$__tool_directory__" # should work generally
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38 template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
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39 template = template_environment.get_template('template_parmconv.j2')
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40 params['fmt'] = '$param_inputs.fmt'
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41 #if str($param_inputs.fmt) == 'AMBER':
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42 params["top_in"] = '$param_inputs.top_in'
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43 #else:
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44 params["top_in"] = '$param_inputs.top_in'
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45 params["str_in"] = '$param_inputs.str_in'
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46 #end if
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47 params['prmtop_ligand'] = '$prmtop_ligand'
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48 params['prmtop_receptor'] = '$prmtop_receptor'
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49 params['prmtop_complex'] = '$prmtop_complex'
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50 params['prmtop_solvatedcomplex'] = '$prmtop_solvatedcomplex'
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51 print(params)
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52
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53
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54 def unescape(cond_text):
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55 """
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56 # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py
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57 """
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58 mapped_chars = { '>' :'__gt__',
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59 '<' :'__lt__',
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60 "'" :'__sq__',
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61 '"' :'__dq__',
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62 '[' :'__ob__',
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63 ']' :'__cb__',
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64 '{' :'__oc__',
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65 '}' :'__cc__',
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66 '@' : '__at__',
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67 '\n' : '__cn__',
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68 '\r' : '__cr__',
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69 '\t' : '__tc__',
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70 '&' : '__and__'
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71 }
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72 for key, value in mapped_chars.items():
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73 cond_text = cond_text.replace( value, key )
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74 return cond_text
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75
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76 def run_template(params=params, system="ligand"):
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77 """
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78 # Render template on a selected system using a local parameter copy
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79 """
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80 localparams=params.copy() # shallow copy ok for simple variables
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81 localparams['stripmask']=unescape(localparams['stripmask_'+system])
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82 localparams['prmtop_out']=localparams['prmtop_'+system]
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83 print(localparams)
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84 with open(system+'.script','w+') as f:
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85 f.write(template.render(localparams))
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86
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87 systems = ['ligand', 'receptor', 'complex', 'solvatedcomplex']
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88 for system in systems:
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89 run_template(system=system)
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90
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91 ]]>
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92 </configfile>
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chemteam
parents:
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93 </configfiles>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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94 <inputs>
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95 <conditional name="param_inputs">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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parents:
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96 <param name="fmt" type="select" label="Force Field format">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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97 <option selected="True" value="AMBER">AMBER</option>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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98 <option value="GROMACS">GROMACS</option>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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99 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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100 <when value="AMBER">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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101 <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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102 </when>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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103 <when value="GROMACS">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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104 <param name="top_in" type="data" label="Input topology (top) file" format="top"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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105 <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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106 </when>
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107 </conditional>
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108 <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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109 <sanitizer>
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110 <valid initial="string.printable">
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111 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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112 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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113 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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114 <add source="&amp;" target="__and__"/>
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115 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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116 </sanitizer>
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117 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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118 <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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119 <sanitizer>
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120 <valid initial="string.printable">
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121 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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122 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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123 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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124 <add source="&amp;" target="__and__"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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125 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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126 </sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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127 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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128 <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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129 <sanitizer>
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130 <valid initial="string.printable">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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131 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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132 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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133 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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134 <add source="&amp;" target="__and__"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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135 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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136 </sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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137 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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138 <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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139 <sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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140 <valid initial="string.printable">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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141 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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142 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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143 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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144 <add source="&amp;" target="__and__"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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145 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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146 </sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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147 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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148 </inputs>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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149 <outputs>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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150 <data format="txt" name="prmtop_ligand" label="ligand prmtop"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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151 <data format="txt" name="prmtop_receptor" label="receptor prmtop"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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152 <data format="txt" name="prmtop_complex" label="complex prmtop"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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153 <data format="txt" name="prmtop_solvatedcomplex" label="solvated complex prmtop"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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154 </outputs>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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155 <tests>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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156 <test>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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157 <!--example in this test is not solvated but sufficient -->
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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158 <param name="fmt" value="AMBER"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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159 <conditional name="param_inputs">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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160 <param name="top_in" value="complex.prmtop"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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161 </conditional>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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162 <param name="stripmask_ligand" value="!:RAL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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163 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT,RAL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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164 <param name="stripmask_complex" value=":NA,CL,SOL,WAT"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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165 <output name="prmtop_ligand">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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166 <assert_contents>
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167 <has_text text=" 61 15"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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168 <has_text text="%FLAG MASS"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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169 <has_text text="RAL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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170 </assert_contents>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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171 </output>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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172 <output name="prmtop_receptor">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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173 <assert_contents>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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174 <has_text text=" 3880 15"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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175 <has_text text="%FLAG MASS"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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176 <has_text text="ALA LEU"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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177 <not_has_text text="RAL "/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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178 </assert_contents>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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179 </output>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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180 <output name="prmtop_complex">
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181 <assert_contents>
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182 <has_text text=" 3941 15"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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183 <has_text text="%FLAG MASS"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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184 <has_text text="ALA LEU"/>
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185 <has_text text="RAL"/>
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186 </assert_contents>
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187 </output>
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188 </test>
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189 <test>
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190 <!--example in this test is from @sbrays' gromacs tests. It has no ligand but is sufficient and will not take extra space in the repo! -->
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191 <param name="fmt" value="GROMACS"/>
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192 <conditional name="param_inputs">
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193 <param name="top_in" value="topol_solv.top"/>
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194 <param name="str_in" value="solv_ions.gro"/>
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195 </conditional>
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196 <!-- pretending CL is a ligand -->
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197 <param name="stripmask_ligand" value="!:CL"/>
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198 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
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199 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
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200 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
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201 <output name="prmtop_ligand">
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202 <assert_contents>
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203 <has_text text=" 8 59"/>
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204 <has_text text="%FLAG MASS"/>
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205 <has_text text="CL"/>
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206 </assert_contents>
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207 </output>
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208 <output name="prmtop_receptor">
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209 <assert_contents>
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210 <has_text text=" 1960 59"/>
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211 <has_text text="%FLAG MASS"/>
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212 <has_text text="LYS VAL PHE "/>
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213 <not_has_text text="CL "/>
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214 </assert_contents>
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215 </output>
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216 <output name="prmtop_solvatedcomplex">
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217 <assert_contents>
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218 <has_text text=" 38265 59"/>
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219 <has_text text="%FLAG MASS"/>
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220 <has_text text="LYS VAL PHE"/>
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221 </assert_contents>
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222 </output>
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223 </test>
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224 </tests>
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225 <help>
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226 <![CDATA[
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227 .. class:: infomark
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228
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229 **What it does**
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230
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231 This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMPBSA calculations.
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232
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233 .. class:: infomark
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234
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235 **How it works**
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236
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237 AmberTools ParmEd is used to strip unneeded atoms and save out the parameter files. The stripmasks are defined by the user.
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238
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239 .. class:: infomark
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240
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241 **Outputs created**
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242
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243 prmtop files for the ligand, receptor, complex and solvated complex.
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244
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245 .. class:: infomark
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246
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247 **User guide and documentation**
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248
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249 - The `AmberTools Manual`_
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250 - The `Parmed Documentation`_
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251
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252
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253 .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf
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254 .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html
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255
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256
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257 ]]>
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258 </help>
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259 <expand macro="citations">
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260 <citation type="bibtex">@misc{parmed_2020, author = {ParmEd}, title = {ParmEd/ParmEd}, url={https://github.com/ParmEd/ParmEd}, abstract = {Parameter/topology editor and molecular simulator. Contribute to ParmEd/ParmEd development by creating an
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261 account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation>
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262 </expand>
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263 </tool>