[Chimera-users] Error while doing autodock vina via chimera

[Sourav Mondal]

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
-----


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.
-----
Application stdout
-----
#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# 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                                                       #
#                                                               #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see http://vina.scripps.edu for more information.      #
#################################################################

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 ... -----


Sent from Mail for Windows 10

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190217/f029076a/attachment.html>