Reply – Re: problem with sdf->pdb conversion
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Re: problem with sdf->pdb conversion
— by Pascal Muller-3 Pascal Muller-3
Dear all,

> Well, I'm starting from an SDF file, which I presume has correct 3D
> coordinates; the reason I used MOL as an intermediate was to use PRODRG
> to produce a "valid" PDB file that I know is correct (this was my
> previous procedure before I discovered OpenBabel).
>
> I've attached the two different PDB files from babel v2.1.1 vs prodrg
> using the same MOL input (in my case, I've included Hs, but it doesn't
> seem make a difference).  My modeling software (Coot) doesn't connect
> the atoms in the same way, so I'm confused.

The only difference I see is atoms order. To answer to Vincent, I
think test.mol is already a 3D conformation, but the molecule is
mostly planar. Prodrg doesn't transform from 2D to 3D.

In my tests with openbabel 2.1.1 :
- Sybyl doesn't read well test-babel.pdb (only 4 atoms are loaded)
- Pymol is OK with test-babel.pdb, but all bonds are single (well, OK,
it's normal)
- Cactvs Browser is OK with test-babel.pdb, the cyclic bonds are
correctly double/single
- Mview (Chemaxon) reads well  test-babel.pdb, but with "~" (any bond)
connection

Starting from a mol2 ligand, converted in pdb by openbabel or
molconvert (Chemaxon):
- Sybyl doesn't read well the ligand.pdb
- Pymol (all single bond) and Cactvs browser (double bonds where needed) are OK
- Mview is unable to load the ligand.pdb...

Again, between ligand.pdb"openbabel" and ligand.pdb converted with
sybyl (starting from mol2), I don't see any difference, apart from
atom ordering.

Hope these small comments could help.

I wish Coot could read mol2, it would help a lot...

By the way, when converting a ligand mol2 in cif, it lost the bond
type information (openbabel 2.1.1). Is there a way to keep bond type
in .cif file when converting with openbabel ? Because mol2->pdb->cif
with eg pdb2cif program is not very useful...

Regards,
Pascal

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