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

[Elaine Meng]

Hi Sourav,
As it says in the error message, the autodock prep cannot handle the MG or NAP residue in the receptor.  Maybe it will work if you delete those residues first.  If they are important for your docking calculations, you may need to find some other method (outside of Chimera).  You could try running the Dock Prep tool before running the Autodock Vina tool in Chimera, but I don’t know if that will help.
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 16, 2019, at 11:51 PM, Sourav Mondal <m.sourav05 at gmail.com> wrote:
> 
> 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