hello guys,
I have a bunch of smiles and I am trying to convert them to mol
the file that I have has 1000 smiles as an example 4 molecules
NC1=CN(N=C(C2=CC(CN(C(C)C3CC3)C4=O)=C4C(C)=C2)C=C5)C5=N1
O=C1N([C@@H](C)C2CC2)CC3=C1C(C)=CC(C(C=C4)=NN5C4=NC(NC(C)=O)=C5)=C3
(CC(C(=O)O)N)CN=C(N)N
> C1=CC=C(C=C1)CC(C(=O)O)N
>
> obabel -i smi test.smi -o mol --gen3d -m
>
> Note the --gen3D command can be slow with a lot of chiral centers.
>
> -Richard
>
> On 5/8/22 18:36, Francois Berenger wrote:
> > On 05/05/2022 05:50, Mohammad
Hello guys,
It has been sometimes that I used obabel but now I cannot use it to convert
lots of molecules to mol format.
I have a MAC and I am trying to convert SMILE to Mol
I do this
obabel .smi -omol -m
This is one example that I save it into a file with format .smi
Hello I have a mac and I want to convert over 1000 files which were
optimized by mopac to hin or mol.
I tried the following
obabel *.out -ohin -m
but it did not work
When I do
user:~ admin$ babel -version
No output file or format spec!
Open Babel 2.0.2 -- Jun 5 2006 -- 14:38:46
Usage:
Hello,
I am wondering if you know a way to convert over 1000 outputs from mopac to
another format like sdf or mol ? each output is a molecule
Many thanks,
Mohammad
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Hello,
I have two questions,
1- I have my molecules as .pdb formats , is it ok? or should I convert them
to another format? if so, should I add hydrogen too?
2- I generate many conformer for each molecules, is there a way to select
the best conformer for lets say 50 molecules ? do you have any
w will fail on linking.
>>
>> Run brew doctor to see if it warns on stuff in /usr/local, especially if
>> there are stuff related to OpenBabel (e.g. libopenbabel, libinchi…)
>>
>> If ”brew link open-babel" fails you can also try with "brew link
>>
