I wrote this reply yesterday, but it didn’t make it to the babble list somehow.
When I try
obabel ~/Desktop/crystal_ligand_flex.sdf -O tst-res.sdf --confab --conf 5
(with your example file), I get a file with 2900 conformers written, so I
believe there is a problem with your installation. Yo
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
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
Can I just check people received the input file? I used the Nabble forum to
attach it ...
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