Gen3d is calling addhydrogen before forcefield calculation, So you might
want to delete some hydrogens afterwards.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/1/21 David García Aristegui
> Hello, i'm unable to generate the 3D coordinates and at the same tim
Hello, i'm unable to generate the 3D coordinates and at the same time add
the polar hydrogens only.
With this command the program adds all hydrogens, polar and non-polar
obabel --AddPolarH --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2
With or without the --AddPolarH flag i retrieve the same out
The problem is solved in the 2.3.2 release!
Thank you very much.
> I'm on trunk version and conversion is successful.
>
> [maciek@fokus ~]$ obabel
> -:"OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12"
> -ismi -omol2 --gen3d
> @MOLECULE
> *
> 65 70
