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6
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1 <tool id="pdb2pqr_plidflow" name="PLIDflow: PDB2PQR">
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2 <description>Converts a pdb to pqr</description>
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3 <inputs>
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4 <param name="receptor_pdb" type="data" format="pdb" label="Receptor PDB file" help="Preparing the receptor involves adding gasteiger charges and adding hydrogens. First it will be processed by pdb2pqr."/>
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5 </inputs>
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6 <command><![CDATA[
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7 swpath=\$(which pdb2pqr.py) ;
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8
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9 ${__tool_directory__}/scripts/preparePDB2PQR_plidflow.sh ${receptor_pdb} ${receptor_pdb}.prepdb ;
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10
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11 (python2.7 \$swpath --ff=amber --ffout=amber --verbose --chain --ph-calc-method=propka --with-ph=7.0 --drop-water ${receptor_pdb}.prepdb ${pdb_processed}.pqr ) &> /dev/null ;
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12
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13 rm ${receptor_pdb}.prepdb ;
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14
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15 ${__tool_directory__}/scripts/includeAtom3.sh ${__tool_directory__}/scripts/table ${pdb_processed}.pqr > ${pdb_processed} ;
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16
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17 rm ${pdb_processed}.pqr ;
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18
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19 ]]></command>
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20 <outputs>
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21 <data name="pdb_processed" format="pdb" label="${receptor_pdb.name}_processed"/>
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22 </outputs>
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23 </tool>
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