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 -0
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 20
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 pret
> "-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill
> valencies, but rather converrts implicit to explicit hydrogens. You
> can open in Avogadro and click "Build/AddHydrogens" to do this.
Well, Avogadro will just call Open Babel. ;-)
> Note to Geoff: would this be a useful 'op' or el
"-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill
valencies, but rather converrts implicit to explicit hydrogens. You
can open in Avogadro and click "Build/AddHydrogens" to do this.
Could I ask you where the XYZ file came from? It may be that a
different route might help.
Note to Geo
Hi Noel,
Many thanks for your answer which is exactly what I'm looking for. However,
for some reason the hydrogens are still not being added when I use the
command. I've attached the CIF file in case I have missed something.
Thanks,
Scott
On 10 September 2012 22:46, Noel O'Boyle wrote:
> (For
(Forgot to cc to the list)
Hi Scott,
The missing information is what bonds connect the heavy atoms as
without this it's not possible to deduce where (and how many) the
hydrogens are. But there should be no need to worry about this. Just
use Open Babel to convert the cif file and add hydrogens:
o
(I forgot to reply to the OpenBabel list the first time, so I'm adding
it to this reply.)
On Sun, Sep 9, 2012 at 3:56 AM, Scott McKechnie wrote:
> Hi Craig,
>
> Many thanks for your reply. Removing the brackets works for some cases but
> unfortunately not all and not the [O][N][C]([C])[C] example
O , 2012-07-31 17:12 +0400, Чугунов Антон rakstīja:
> Dear open babel users,
> I'm adding hydrogens in python script
> using pep.OBMol.AddHydrogens(False, True, 7) function (where pep is
> pybel molecule). But after saving this to PDB file I've got a problem:
> all hydrogens are written AFTER all h
On Tue, Jul 31, 2012 at 6:12 AM, Чугунов Антон wrote:
> Dear open babel users,
> I'm adding hydrogens in python script using pep.OBMol.AddHydrogens(False,
> True, 7) function (where pep is pybel molecule). But after saving this to
> PDB file I've got a problem: all hydrogens are written AFTER all
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