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<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">Hello<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present
is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1)<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">from DockPrep import prep<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">model=Midas.open('4iaq.pdb')<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">prep(model)<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">modelname='4iaq.mol2'<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">from WriteMol2 import writeMol2<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">writeMol2(model, modelname)<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">#VinaRun<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq'<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true")<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering.<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">The 4iaq.receptor.pdbqt file contains the
<i>unmodified</i> protein with charges etc, and with the original PDB residue numbering.<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">The 4iaq.mol2 file contains the
<i>modified</i> protein, with charges etc, but with residue numbering modified to start at 1.<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">What I hoped to produce was a 4iaq.receptor.pdbqt file containing the
<i>modified</i> protein with charges etc, and with the <i>original</i> PDB residue numbering, and this is just about the only thing I don’t have.
<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">Any help would be very gratefully received.<o:p></o:p></span></p>
<p class="MsoNoSpacing"><span style="font-family:"Times New Roman","serif"">Anthony
<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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