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--></style></head><body lang=EN-IN link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>I was tring to dock the phytochemical (cid-3114) with protein (pdb id -5YFN) , this is the error I am getting. What is the reason for the error? How to overcome this error?</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Model 0 (human isocitrate dehydrogenase.pdb) appears to be a protein without secondary structure assignments.</p><p class=MsoNormal>Automatically computing assignments using 'ksdssp' and parameter values:</p><p class=MsoNormal> energy cutoff -0.5</p><p class=MsoNormal> minimum helix length 3</p><p class=MsoNormal> minimum strand length 3</p><p class=MsoNormal>Use command 'help ksdssp' for more information.</p><p class=MsoNormal>No SEQRES records for human isocitrate dehydrogenase.pdb (#0) chain C; guessing terminii instead</p><p class=MsoNormal>Chain-initial residues that are actual N terminii: </p><p class=MsoNormal>Chain-initial residues that are not actual N terminii: #0 LYS 1.C</p><p class=MsoNormal>Chain-final residues that are actual C terminii: #0 MG 410.C</p><p class=MsoNormal>Chain-final residues that are not actual C terminii: </p><p class=MsoNormal>396 hydrogen bonds</p><p class=MsoNormal>Hydrogens added</p><p class=MsoNormal>Wrote E:\Sem 1\BIOINFO\human_isd_3114.receptor.pdb</p><p class=MsoNormal>Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2B</p><p class=MsoNormal>Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2D</p><p class=MsoNormal>Unable to assign MAP type to atom Mg</p><p class=MsoNormal>Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:MG 410:MG</p><p class=MsoNormal>Wrote E:\Sem 1\BIOINFO\human_isd_3114.ligand.pdb</p><p class=MsoNormal>Autodock Vina ligand docking initiated for human isocitrate dehydrogenase.pdb</p><p class=MsoNormal>Status file contents:</p><p class=MsoNormal>1</p><p class=MsoNormal>1550389354.82</p><p class=MsoNormal>1550389354.92</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Running AutoDock Vina for human isocitrate dehydrogenase.pdb failed; see Reply Log for more information</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Application stderr</p><p class=MsoNormal>-----</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Parse error on line 4016 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.</p><p class=MsoNormal>-----</p><p class=MsoNormal>Application stdout</p><p class=MsoNormal>-----</p><p class=MsoNormal>#################################################################</p><p class=MsoNormal># If you used AutoDock Vina in your work, please cite: #</p><p class=MsoNormal># #</p><p class=MsoNormal># O. Trott, A. J. Olson, #</p><p class=MsoNormal># AutoDock Vina: improving the speed and accuracy of docking #</p><p class=MsoNormal># with a new scoring function, efficient optimization and #</p><p class=MsoNormal># multithreading, Journal of Computational Chemistry 31 (2010) #</p><p class=MsoNormal># 455-461 #</p><p class=MsoNormal># #</p><p class=MsoNormal># DOI 10.1002/jcc.21334 #</p><p class=MsoNormal># #</p><p class=MsoNormal># Please see http://vina.scripps.edu for more information. #</p><p class=MsoNormal>#################################################################</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>WARNING: The search space volume > 27000 Angstrom^3 (See FAQ)</p><p class=MsoNormal>Detected 8 CPUs</p><p class=MsoNormal>WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs</p><p class=MsoNormal>Reading input ... -----</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p></div></body></html>