GCC 4.8.2 is known to be problematic with C++ and is also an ancient
compiler.
https://www.gnu.org/software/gcc/gcc-4.8/
The original release was in 2013 (10 years ago).
Please install a more recent version of GCC / G++
Best regards,
-Geoff
On Jun 8, 2023 at 1:34:12 PM, Alessandro S. Nasciment
I doubt you can do this. Open Babel 2.4.1 was from 2016 or so? Compilers
have changed.
The current version of Open Babel is 3.1.1 and it definitely compiles on my
Mac. You can install with homebrew or conda, etc. if you don’t want to
compile yourself.
-Geoff
---
Prof. Geoffrey Hutchison
The pip recipe is to build the openbabel python bindings from source. That
requires that openbabel has been built and installed from source before you
run the pip build.
Personally, I’d suggest using mamba-forge and their openbabel package.
Best,
-Geoff
On Jul 31, 2023 at 5:04:11 AM, Tim Dudgeo
.
obabel -:'CCC.C=O' -O test.xyz —gen3d
See attached.
Best,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchisonlab.org/
On Jul 25, 2023 at 1:58:18 PM, Alan Liška wrot
44773296/libstdc-so-6-version-glibcxx-3-4-20-not-found
Best regards,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchisonlab.org/
___
Open
I think you’re mixing up “obminimize” which is a specific tool, and
“obabel” which can convert, etc.
I’d suggest something like:
obabel {input_file} -O {output_file} -opdbqt --minimize -sd -ff GAFF -h
Best,
-Geoff
On Aug 8, 2023 at 2:24:21 PM, Lock Meister wrote:
> Hi,
>
> I was trying to r
ing to
adjust protonation for all functional groups?
That’s not what Open Babel does .. it has a set of rules, particularly for
amino acids.
At the moment, you may want to look at Dimorphite:
https://github.com/durrantlab/dimorphite_dl/blob/master/README.md
Hope that helps,
-Geoff
---
Prof. Geof
Unfortunately, as part of a routine hosting update (e.g., my provider
changed DNS) the openbabel.org website is currently down.
It’s not clear from the logs why the site remains down.
I’m going to take the opportunity to cleanup a new website based on Noel
O’Boyle’s excellent docs: https://open-b
The MAE parser has some definite issues.
Try running “ccmake” to turn off WITH_MAEPARSER or run “cmake
-DWITH_MAEPARSER=OFF”
Hope that helps,
-Geoff
On Nov 2, 2023 at 2:00:12 PM, Dhruv J wrote:
> Hello everyone,
> I am Dhruv, a third year Computer Engineering undergrad from Mumbai,
> India. I
you please suggest any of the issues from which I can get
> started with my contributions to openbabel
>
> On Fri, Nov 3, 2023 at 3:12 AM Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
>
>> The MAE parser has some definite issues.
>>
>>
Dear David,
Of course we are happy to have an updated forcefield - I’m sure others will
use it.
Out of curiosity, does this include the polarizable electrostatics or does
it just use whatever partial charges are assigned already?
Thanks and best regards,
-Geoff
---
Prof. Geoffrey Hutchison
ire stereo is be
reperceived, then OBMol::SetChiralityPerceived(false) should be called.”
Best regards,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: https://hutchisonlab.org/
__
I don’t think at the moment, we have something that copies any entries
with errors. It’s a useful idea.
-Geoff
On Feb 11, 2025 at 4:06:09 AM, Chris Swain via OpenBabel-discuss <
openbabel-discuss@lists.sourceforge.net> wrote:
> Hi,
>
> I want to convert some very large sdf files to SMILES. I k
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