It seems this bug came back a few times in the past:
https://sourceforge.net/p/openbabel/bugs/710/
S
On 06/19/2018 09:09 AM, Geoffrey Hutchison wrote:
We're not responsible for Autodock - you might want to contact them.
As far as small molecules getting large total charges, that's a bug - c
We're not responsible for Autodock - you might want to contact them.
As far as small molecules getting large total charges, that's a bug - can you
give us an example and file it at:
https://github.com/openbabel/openbabel/issues
Thanks and best regards,
-Geoff
> On Jun 14, 2018, at 8:44 AM, Mich
Hi,
According to the 2006 J Comput Chem paper describing Autodock 4, OpenBabel
was used to add hydrogens and assign Gasteiger charges to the protein and
ligands that were used as the training set to calibrate the force field. I
just want to ask whether the -p option in OB was used to do this (wher
Sorry, I meant to cc the list in.
Quoting Noel O'Boyle on Wed, 23 Nov 2011
20:06:40 +0100:
> There seems to be a series of related issues. By the way, you should
> really email the list, so that people are aware you want something
> done about it.
>
> - Noel
>
> On 23 November 2011 19:33, Doug
I tried to do this but I get a 500 Internal Server Error when I try to
use the 'Add new' link here:
http://sourceforge.net/tracker/?atid=428740&group_id=40728&func=browse
Quoting Noel O'Boyle :
> Please go ahead - it's the only way to ensure that issues like this
> don't fall between the cra
Please go ahead - it's the only way to ensure that issues like this
don't fall between the cracks...
On 3 March 2011 10:50, Douglas Houston wrote:
> OK, just to follow up on this, if no-one has any objections I will
> submit a bug report.
>
>
> Quoting "Mathias W." :
>
>> Yeah, thats because I'm
OK, just to follow up on this, if no-one has any objections I will
submit a bug report.
Quoting "Mathias W." :
> Yeah, thats because I'm stupid - I didn't recognize that all these
> numbers were recognized as text :-(
>
> 2010/12/3 Douglas Houston :
>> That's strange, if I sum everything in th
Yeah, thats because I'm stupid - I didn't recognize that all these
numbers were recognized as text :-(
2010/12/3 Douglas Houston :
> That's strange, if I sum everything in the charge column in your
> molecule_H.mol2 file, I get -9.0 ...
>
>
>
> Quoting "Mathias W." :
>
>> Servus,
>>
>> I get both
That's strange, if I sum everything in the charge column in your
molecule_H.mol2 file, I get -9.0 ...
Quoting "Mathias W." :
> Servus,
>
> I get both times over all charge zero (with ob-2.2.3)
>
> (molecule_H2.mol2 was produced with -h)
>
>
> 2010/12/3 Douglas Houston :
>> Hi all,
>>
>> Just
Servus,
I get both times over all charge zero (with ob-2.2.3)
(molecule_H2.mol2 was produced with -h)
2010/12/3 Douglas Houston :
> Hi all,
>
> Just wondering if anyone got a chance to test this molecule? I want to
> make sure it's not just my installation ...
>
> cheers,
>
> Doug
--
M
Hi all,
Just wondering if anyone got a chance to test this molecule? I want to
make sure it's not just my installation ...
cheers,
Doug
Quoting Douglas Houston :
> Hi,
>
> I have observed something curious about variations in the way
> OpenBabel assigns Gasteiger charges.
>
> For exampl
Hi,
I have observed something curious about variations in the way
OpenBabel assigns Gasteiger charges.
For example,
babel -isdf molecule.sdf -omol2 molecule_H.mol2 -h
produces a molecule with an overall charge that is essentially 0.
However, the command
babel -isdf molecule.sdf -omol2 m
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