Hello again,
I also found out that there is problem with atom typing, which is bypassed
while converting molecules (as in my previous reply). The nitrogen should
be planar (N.pl3 as in mol2) and its' conformation in sdf file which you've
provided is
sp3.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-05-13 14:06 GMT+02:00 Maciek Wójcikowski <mac...@wojcikowski.pl>:
> We've received the input file. Of course there is problem with it, when
> you pass it through mol2 file, then your fine. Also obabel reports "-nan"
> scores for original molecule, which is bad.
>
> obabel crystal_ligand_flex.sdf -omol2 | obabel -imol2 --conformer --nconf
> 2 --writeconformers -o smi
>
> Above command will output 2 conformets. I can't pin-point the problem with
> this molecule yet,but still there is a solution.
>
> ----
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> 2014-05-13 13:38 GMT+02:00 Douglas Houston <dhous...@staffmail.ed.ac.uk>:
>
> Can I just check people received the input file? I used the Nabble forum to
>> attach it ...
>>
>>
>>
>> --
>> View this message in context:
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>> Sent from the General discussion mailing list archive at Nabble.com.
>>
>>
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