Mercurial > repos > chemteam > parmconv

annotate parmconv.xml @ 0:6c6cecf51bd0 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
author chemteam
date Tue, 07 Apr 2020 08:07:39 -0400
parents
children da2252f1ccab
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6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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1 <tool id="parmconv" name="Convert Parameters" version="@VERSION@">
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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 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="3.2.0">parmed</requirement>
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8 <requirement type="package" version="2019.1">gromacs</requirement>
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9 <requirement type="package" version="2.11.1">jinja2</requirement>
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10 </expand>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 python '$templating_script' '$inputs' &&
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14 PATH_TO_PARMED=\$(dirname `which parmed`) &&
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15 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) &&
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16 export GMXDATA=\$AMBERHOME/share/gromacs/top/ &&
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17 parmed -i ligand.script -O &&
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18 parmed -i receptor.script -O &&
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19 parmed -i complex.script -O &&
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20 parmed -i solvatedcomplex.script -O
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21
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22 ]]>
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23 </command>
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24 <configfiles>
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25 <inputs name="inputs"/>
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26 <configfile name="templating_script">
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27 <![CDATA[
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28
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29 import os
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30 import sys
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31 import json
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32
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33 from jinja2 import Environment, FileSystemLoader
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34 input_json_path = sys.argv[1]
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35 params = json.load(open(input_json_path, "r"))
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36 currentpath = "$__tool_directory__" # should work generally
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37 template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
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38 template = template_environment.get_template('template_parmconv.j2')
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39 params['fmt'] = '$param_inputs.fmt'
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40 #if str($param_inputs.fmt) == 'AMBER':
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41 params["top_in"] = '$param_inputs.top_in'
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42 #else:
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43 params["top_in"] = '$param_inputs.top_in'
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44 params["str_in"] = '$param_inputs.str_in'
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45 #end if
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46 params['prmtop_ligand'] = '$prmtop_ligand'
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47 params['prmtop_receptor'] = '$prmtop_receptor'
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48 params['prmtop_complex'] = '$prmtop_complex'
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49 params['prmtop_solvatedcomplex'] = '$prmtop_solvatedcomplex'
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50 print(params)
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51
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52
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53 def unescape(cond_text):
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54 """
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55 # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py
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56 """
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57 mapped_chars = { '>' :'__gt__',
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58 '<' :'__lt__',
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59 "'" :'__sq__',
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60 '"' :'__dq__',
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61 '[' :'__ob__',
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62 ']' :'__cb__',
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63 '{' :'__oc__',
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64 '}' :'__cc__',
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65 '@' : '__at__',
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66 '\n' : '__cn__',
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67 '\r' : '__cr__',
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68 '\t' : '__tc__',
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69 '&' : '__and__'
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70 }
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71 for key, value in mapped_chars.items():
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72 cond_text = cond_text.replace( value, key )
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73 return cond_text
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74
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75 def run_template(params=params, system="ligand"):
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76 """
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77 # Render template on a selected system using a local parameter copy
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78 """
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79 localparams=params.copy() # shallow copy ok for simple variables
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80 localparams['stripmask']=unescape(localparams['stripmask_'+system])
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81 localparams['prmtop_out']=localparams['prmtop_'+system]
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82 print(localparams)
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83 with open(system+'.script','w+') as f:
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84 f.write(template.render(localparams))
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85
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86 systems = ['ligand', 'receptor', 'complex', 'solvatedcomplex']
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87 for system in systems:
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88 run_template(system=system)
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89
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90 ]]>
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91 </configfile>
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92 </configfiles>
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93 <inputs>
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chemteam
parents:
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94 <conditional name="param_inputs">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
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95 <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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96 <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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97 <option value="GROMACS">GROMACS</option>
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98 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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99 <when value="AMBER">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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100 <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"
chemteam
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101 </when>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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102 <when value="GROMACS">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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103 <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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104 <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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105 </when>
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106 </conditional>
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107 <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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108 <sanitizer>
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109 <valid initial="string.printable">
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110 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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111 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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112 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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113 <add source="&amp;" target="__and__"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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114 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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115 </sanitizer>
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116 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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117 <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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118 <sanitizer>
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119 <valid initial="string.printable">
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120 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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121 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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122 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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123 <add source="&amp;" target="__and__"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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124 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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125 </sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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126 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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127 <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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128 <sanitizer>
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129 <valid initial="string.printable">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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130 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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131 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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132 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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133 <add source="&amp;" target="__and__"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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134 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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135 </sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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136 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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137 <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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138 <sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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139 <valid initial="string.printable">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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140 <remove value="&amp;"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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141 </valid>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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142 <mapping initial="none">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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143 <add source="&amp;" target="__and__"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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144 </mapping>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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145 </sanitizer>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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146 </param>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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147 </inputs>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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148 <outputs>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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149 <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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150 <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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151 <data format="txt" name="prmtop_complex" label="complex prmtop"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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152 <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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153 </outputs>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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154 <tests>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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155 <test>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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156 <!--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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157 <param name="fmt" value="AMBER"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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158 <conditional name="param_inputs">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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159 <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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160 </conditional>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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161 <param name="stripmask_ligand" value="!:RAL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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162 <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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163 <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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164 <output name="prmtop_ligand">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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165 <assert_contents>
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166 <has_text text=" 61 15"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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167 <has_text text="%FLAG MASS"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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168 <has_text text="RAL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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169 </assert_contents>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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170 </output>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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171 <output name="prmtop_receptor">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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172 <assert_contents>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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173 <has_text text=" 3880 15"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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174 <has_text text="%FLAG MASS"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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175 <has_text text="ALA LEU"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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176 <not_has_text text="RAL "/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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177 </assert_contents>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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178 </output>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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179 <output name="prmtop_complex">
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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180 <assert_contents>
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181 <has_text text=" 3941 15"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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182 <has_text text="%FLAG MASS"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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183 <has_text text="ALA LEU"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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184 <has_text text="RAL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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185 </assert_contents>
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186 </output>
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187 </test>
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188 <test>
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189 <!--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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190 <param name="fmt" value="GROMACS"/>
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191 <conditional name="param_inputs">
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192 <param name="top_in" value="topol_solv.top"/>
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193 <param name="str_in" value="solv_ions.gro"/>
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194 </conditional>
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195 <!-- pretending CL is a ligand -->
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196 <param name="stripmask_ligand" value="!:CL"/>
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197 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
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198 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
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199 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
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200 <output name="prmtop_ligand">
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201 <assert_contents>
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202 <has_text text=" 8 59"/>
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203 <has_text text="%FLAG MASS"/>
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204 <has_text text="CL"/>
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205 </assert_contents>
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206 </output>
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207 <output name="prmtop_receptor">
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208 <assert_contents>
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209 <has_text text=" 1960 59"/>
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210 <has_text text="%FLAG MASS"/>
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211 <has_text text="LYS VAL PHE "/>
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212 <not_has_text text="CL "/>
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213 </assert_contents>
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214 </output>
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215 <output name="prmtop_solvatedcomplex">
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216 <assert_contents>
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217 <has_text text=" 38265 59"/>
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218 <has_text text="%FLAG MASS"/>
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219 <has_text text="LYS VAL PHE"/>
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220 </assert_contents>
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221 </output>
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222 </test>
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223 </tests>
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224 <help>
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225 <![CDATA[
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226 .. class:: infomark
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227
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228 **What it does**
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229
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230 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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231
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232 .. class:: infomark
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233
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234 **How it works**
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235
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236 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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237
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238 .. class:: infomark
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239
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240 **Outputs created**
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241
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242 prmtop files for the ligand, receptor, complex and solvated complex.
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243
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244 .. class:: infomark
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245
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246 **User guide and documentation**
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247
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248 - The `AmberTools Manual`_
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249 - The `Parmed Documentation`_
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250
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251
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252 .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf
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253 .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html
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254
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255
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256 ]]>
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257 </help>
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258 <expand macro="citations">
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259 <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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260 account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation>
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261 </expand>
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262 </tool>