[Chimera-users] AutoDock Vina error on Chimera

[Utkarsh Narsaria]

Dear Dr. Meng,

Thank you for your reply. I was able to resolve the Hc-Hc atom type error
with your suggestions. But for the Hn atom type, the error is persistent. I
cannot delete these atoms as they are important for docking. Hence, I am
attaching the ligand file in the MOL2 format and snip of the ligand with Hn
atom type with this mail for your reference. I would like to know your
valuable input in resolving the error.

Regards,
Utkarsh


On Fri, Jun 24, 2022 at 9:34 PM Elaine Meng <elaine.meng at ucsf.edu> wrote:

> Hello Utkarsh,
> Autodock Vina only works with the usual common elements.  Those messages
> from Autodock Vina are saying that it does not recognize atom types Ho
> (holmium??) and Hc (which is not even an element symbol).  Without your
> providing an example input that shows the problem, my only guess is that
> you have hydrogens with 4-character atom names that start with HO and HC
> which makes Autodock scripts guess that they are different elements
> (instead of hydrogen).   I don't know if Chimera added those hydrogens or
> if they were already in your ligand files when you opened them.
>
> Autodock Vina is developed by another group and and so we are not experts
> in that program.  However, my understanding is that it doesn't use atomic
> charges and doesn't use hydrogens on carbons.  So you may not need to use
> Dock Prep at all, because the Autodock Vina tool already has an option to
> add hydrogens in Chimera (see the "Receptor options" in the tool).
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
> >
>
> However, you could turn off that option in the Autodock Vina tool if you
> wanted just to run addh separately beforehand.  That would also allow you
> to delete the nonpolar ( = those on carbon) hydrogens before using Autodock
> Vina, e.g. command
>
> delete HC
>
> ...which should get rid of the "Hc" type messages.  You don't want to
> delete the hydrogens on oxygen even though it would prevent "Ho" messages,
> since they are needed for atom type identification.  Instead you would have
> to either manually edit your ligand atom names to avoid 4-character
> hydrogen names starting with HO (if my theory that 4-character atom names
> are the problem is correct).
>
> Please note that the Autodock Vina tool in Chimera is of limited use, as
> mentioned in the gray box at the top of the help page:
>
> "this tool only allows docking a single ligand with very limited sampling.
> For a more intensive sampling of space, as needed for most research
> applications, or access to other options such as ligand database search, we
> recommend running the locally installed copy of AutoDock Vina directly (not
> using Chimera)."
>
> I hope this helps,
> Elaine
>
> > On Jun 24, 2022, at 3:28 AM, Utkarsh Narsaria via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Team,
> > I am using chimera for a typical protein-ligand docking study. The
> ligands were prepared in chimera itself using the dockprep options using
> gasteiger charges and amber ff14SB force field. While docking the same
> using AutoDock Vina function in Chimera , we encountered few errors for
> some of the ligands. The errors are explained as follows :
> > 1. "" Ho" is not a valid dock type AutoDock atom types are
> case-sensitive."
> > 2. Autodock Vina Error on Chimera: "ValueError: Could not find an atomic
> number for Hc Hc"
> > Any inputs regarding these will be helpful in resolving the issues.
> > Regards,
> > Utkarsh
>
>
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