Hi,
I am trying to use minimization feature using uff but it is adding hydrogens to
fill the shell. How do I prevent from addition of any additional atoms beyond
what is in the input file.
Here is a same input and the command I am using.
Input.mol
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 -0.0000 -0.0000 Li 0 0 0 0 0 0 0 0 0 0 0 0
0.4622 -0.2286 -0.0600 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.4434 0.2193 0.0576 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
M END
Command: obabel input.mol -O output.mol --minimize --steps 10000 --sd --ff uff
output.mol:
OpenBabel03302314253D
5 4 0 0 0 0 0 0 0 0999 V2000
-0.0207 -0.0375 -0.0870 Li 0 0 0 0 0 0 0 0 0 0 0 0
1.7549 -0.3412 -0.5469 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.7957 0.2668 0.3744 O 0 0 0 0 0 0 0 0 0 0 0 0
2.2720 0.2359 0.0697 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.7870 0.3281 1.3627 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 4 1 0 0 0 0
3 5 1 0 0 0 0
M END_______________________________________________
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