ligand charges question

[Paul Charifson]

If I use an SDF file for ligand input does this mean that there will be no charges assigned or will the program assign charges to the ligand ? Alternatively, if I used an input format that possesses a charge field (e.g. mol2), which charge model is recommended ?

Thank you,
Paul

[David Koes]

The default Vina scoring function does not use partial charges, so it is mute. If you provide a file format that includes partial charges (e.g. pdbqt) then those will be used. Otherwise OpenBabel is used to copute Gasteiger charges. Again, this is only relevant if you are using a custom scoring function that uses charges.

[Paul Charifson]

Dave,

Thank you for the response. Does the Vinardo scoring function us
partial charges ?

Paul

On Sun, Mar 22, 2020 at 1:22 PM David Koes dkoes@users.sourceforge.net
wrote:

The default Vina scoring function does not use partial charges, so it is
mute. If you provide a file format that includes partial charges (e.g.
pdbqt) then those will be used. Otherwise OpenBabel is used to copute
Gasteiger charges. Again, this is only relevant if you are using a custom
scoring function that uses charges.

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ligand charges question
https://sourceforge.net/p/smina/discussion/help/thread/e1db5dffd0/?limit=25#05af

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[Paul Charifson]

Thank you for the response. Does the Vinardo scoring function implemented in Smina use partial charges ?

Paul

[David Koes]

No. vinardo is a re-parameterization of vina. It does not add new terms.