Hi Hetal,
As I always comment, "OB is not adding hydrogens. The hydrogens are already
there, just implicit." That is, your original MOL file is in fact Li(OH)2
(but you can't tell that unless you are familiar with the MOL file spec).
How are you creating the input file? Is there a way to set the
Hello.
I'm a doctoral student and I'm using openbabel for my thesis. Currently, I
want to prepare a ligand for my molecular docking. For this, I take the
ligand in SMILES format and converted it to SDF or MOL format.
With scripts of the tutorial:
PROMPT> obabel -ismi 'outputfile.smi' -osdf 'mymol
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