Thanks - Vina is being used, and if all H are not added before energy
minimization, it appears that results are off (e.g. long CH2 chains will look
like a loose rope). Yes, Vina only leaves polar H in the resulting pdbqt files.
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On Sat, Nov 3, 2018 at 6:38 AM
Hi,
This is highly dependent on docking software. Autodock Vina requires only
polar hydrogens, but others will differ.
Best,
Maciek
sob., 3 lis 2018, 11:28: Noel O'Boyle napisał(a):
> You need to add all hydrogens. I have never understood why those options
> are provided.
>
> On Thu, 1 Nov
You need to add all hydrogens. I have never understood why those options
are provided.
On Thu, 1 Nov 2018, 19:41 Leif Peterson Before performing ligand energy minimization then docking with receptors,
> I am adding hydrogens to ligands via the syntax:
>
> Addhydrogens(False, False);
>
> I am
Think about cells or stomachs or whatever having a certain pH due to the
presence of acids and bases. Your molecule will be protonated according to
this pH.
On Thu, 1 Nov 2018, 19:52 Leif Peterson For stripping the counter ion of a salted ligand, I am basically using the
> larger smiles string
