<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--></head><body lang=DE link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Hi everyone,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>I’m using Chimera 1.11.2 on windows.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>I am experience following error after my workflow.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I fetched a known pdb model from the servers and generated several structural models of similar sequences using the integrated MODELLER script.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Since my pdb model contains a covalently attached cofactor in the active site, I let MODELLER include non-water HETATM into my structural models as well.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Afterwards I tried to do substrate/product binding studies with the known pdb model as well as with the generated structural models using the AutoDockVina script.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>However, when I run the script with the known pdb model, everything works fine.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>But when I’m running the script with the structural models, I receive following error msg:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>“Parse error on line 8553 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.”<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>It should be noted that this error does not occur if I won’t include non-water HETATM by MODELLER. Makes sense, since having a look at the generated pdbqt file, the FAD lines are generating the error. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>“<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HETATM 8554 HO3' FAD 525 62.339 60.023 -29.788 1.00 0.00 0.238 Ho<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HETATM 8555 HO2' FAD 525 66.741 58.106 -28.406 1.00 0.00 0.397 Ho<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HETATM 8556 HO3B FAD 525 60.634 66.984 -32.274 1.00 0.00 0.221 Ho<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HETATM 8557 HO4' FAD 525 65.182 62.428 -29.602 1.00 0.00 0.217 Ho<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HETATM 8558 1H6A FAD 525 68.751 67.392 -38.565 1.00 0.00 0.157 HD<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HETATM 8559 2H6A FAD 525 68.156 65.783 -38.183 1.00 0.00 0.157 HD<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HETATM 8560 HO2B FAD 525 62.183 68.217 -34.408 1.00 0.00 0.253 Ho<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>“<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I found that AutoDockVina needs a “HD” instead of a “Ho” entry at these positions? Is this correct?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>So my question is, why is AutoDock vina generating a pdbqt file in the first place which it cannot read properly in the next step?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>How can I prevent this? I cannot just change the pdbqt entries as AutoDockVina will overwrite it again.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Thanks in advance for any help!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Bastian</span><span style='font-size:9.0pt;font-family:"Arial","sans-serif";mso-fareast-language:DE'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>