On Oct 22, 2021, at 10:40, Francesca Magarotto -
[email protected] <[email protected]>
wrote:
> I need this file in TRIPOS MOL2 format, but I've read on the documentation
> that mol2 is SYBYL MOL2 format. Are they the same?
Sybyl was a tool sold by Tripos. They are the same thing.
> For the conversion, I used the command: obabel -i smi inputfile.smi -o mol2
> -O outputfile.mol2 --gen3D.
> I heve another question related to hydrogens atoms: I know that in SMILES
> format hydrogens are not normally explicitly represented, but I need them in
> order to perform docking and virtual screening.
> I didn't write the option -h in the command I used for the conversion, but
> when I look at the graphic representation of some molecules I see the
> hydrogens. It seems to me that (even without the -h option) the hydrogens are
> added explicitly.
> Is that correct?
Sure looks like it.
% echo "C methane" > methane.smi
% cat methane.smi
C methane
% obabel -i smi methane.smi -o mol2 -O methane.mol2 --gen3D
1 molecule converted
% cat methane.mol2
@<TRIPOS>MOLECULE
methane
5 4 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 0.9240 -0.0178 0.0625 C.3 1 UNL1 -0.0776
2 H 2.0162 -0.0178 0.0625 H 1 UNL1 0.0194
3 H 0.5599 0.4927 0.9568 H 1 UNL1 0.0194
4 H 0.5599 -1.0475 0.0575 H 1 UNL1 0.0194
5 H 0.5599 0.5014 -0.8268 H 1 UNL1 0.0194
@<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 1
4 1 5 1
I am far from an expert on the Open Babel internals, but checking the source,
it looks like the AddHydrogen() is part of the gen3d() call:
% grep --context=3 AddHydrogen ./src/ops/gen3d.cpp
// rule-based builder worked
molCopy.SetDimension(3);
molCopy.AddHydrogens(false, false); // Add some hydrogens before running
MMFF
if (speed == 5)
return true; // done
> If someone has already used ZINC15 to download libraries,
I haven't done that.
Cheers,
Andrew
[email protected]
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