hmm, strange.
how do you look at the structure?
creating a svg with obabel and -osvg actually seems to
repair the problem when the input is a mol2 file but not if it's a pdb file
could you try this:
obabel -ismi 454.smi -O 454.mol2 --gen3D -h
obminimize -ff GAFF -o pdb 454.mol2 > 454-gaff.pdb
On 09/01/17 17:57, Eiso AB wrote:
> hmm, strange.
> how do you look at the structure?
Generate an sdf with babel instead of a mol2 and then visualize with
avogadro (pdb with pymol works just as well).
We will look into the GAFF atom typing (my group did the last update).
> creating a svg with o
On 09/01/17 16:08, Eiso AB wrote:
> (installation: Open Babel 2.4.0)
>
> I'm getting a distorted ring (the 5-ring) when using
> obminimize with -ff GAFF
>
> 454.smi
> OC1=CC=C(C=C1)C2=NN=C(O2)SCC#C
>
> obabel -ismi 454.smi -O 454.mol2 --gen3D -h
> obminimize -ff GAFF -o mol2 454.mol2 > 454-gaff.mol
(installation: Open Babel 2.4.0)
I'm getting a distorted ring (the 5-ring) when using
obminimize with -ff GAFF
454.smi
OC1=CC=C(C=C1)C2=NN=C(O2)SCC#C
obabel -ismi 454.smi -O 454.mol2 --gen3D -h
obminimize -ff GAFF -o mol2 454.mol2 > 454-gaff.mol2
when -ff GAFF is omitted the results look ok.
I
