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?

Model 0 (human isocitrate dehydrogenase.pdb) appears to be a protein without secondary structure assignments.

Automatically computing assignments using 'ksdssp' and parameter values:

  energy cutoff -0.5

  minimum helix length 3

  minimum strand length 3

Use command 'help ksdssp' for more information.

No SEQRES records for human isocitrate dehydrogenase.pdb (#0) chain C; guessing terminii instead

Chain-initial residues that are actual N terminii:

Chain-initial residues that are not actual N terminii: #0 LYS 1.C

Chain-final residues that are actual C terminii: #0 MG 410.C

Chain-final residues that are not actual C terminii:

396 hydrogen bonds

Hydrogens added

Wrote E:\Sem 1\BIOINFO\human_isd_3114.receptor.pdb

Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2B

Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2D

Unable to assign MAP type to atom Mg

Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:MG 410:MG

Wrote E:\Sem 1\BIOINFO\human_isd_3114.ligand.pdb

Autodock Vina ligand docking initiated for human isocitrate dehydrogenase.pdb

Status file contents:

1

1550389354.82

1550389354.92

Running AutoDock Vina for human isocitrate dehydrogenase.pdb failed; see Reply Log for more information

Application stderr

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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.

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Application stdout

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# If you used AutoDock Vina in your work, please cite:          #

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# O. Trott, A. J. Olson,                                        #

# AutoDock Vina: improving the speed and accuracy of docking    #

# with a new scoring function, efficient optimization and       #

# multithreading, Journal of Computational Chemistry 31 (2010)  #

# 455-461                                                       #

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# DOI 10.1002/jcc.21334                                         #

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WARNING: The search space volume > 27000 Angstrom^3 (See FAQ)

Detected 8 CPUs

WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs

Reading input ... -----

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