Hi,
> I would like Babel to have numbers in atom names when converting PDB to
> MOL2. For example, this is a real output:
> 45 C36 9.9680 -15.9360 -13.8330 C.3 100 AB1100
> -0.0362
> 46 C37 17.5010 -27.1690 -17.2360 C.3 100 AB1100
> -0.0214
> 47 H 19.5093 -27.3124 -16.5262 H 100 AB1100
> 0.0463
> 48 H 18.4112 -26.4295 -15.4641 H 100 AB1100
> 0.0463
> 49 H 15.7497 -26.3886 -18.1782 H 100 AB1100
> 0.0466
>
> and this is the output I want (I get this file by using PRODGR server):
> 79 C30 8.945 -15.719 -14.923 C.ar 1 AB1 -0.037
> 80 C36 9.968 -15.936 -13.833 C.3 1 AB1 0.114
> 81 H9Y 9.477 -16.349 -12.952 H 1 AB1 -0.021
> 82 H9Z 10.377 -14.943 -13.645 H 1 AB1 -0.021
> 83 H36 10.731 -16.631 -14.183 H 1 AB1 -0.021
>
> I want to get the atom names because when I run APBS to find the
> electrostatic potential, it finds that the H atoms are duplicated and
> doesn't include them on its calculation.
>
>
"H" is a good atom name for hydrogens in mol2 format, as far as I know, and
there is no reason to add numbers in the atom name, although such names
will still be correct.
I don't know APBS, but there is no reason to consider H atoms as
duplicates...
Anyway, for ligands, starting from pdb format is not a good idea, even with
PRODRG. You should find a better format (smiles, sdf, mol2) on e.g. the PDB
website
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=AB1
or
http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/AB1
> Also, aren't that H atoms misalign? They should have two space after
> number line, not one.
>
If you mean the number of spaces between atom_id (e.g. 45 in your first
line) and atom_name (e.g. C36 in your first line), one space is enough if I
don't misunderstand the documentation:
http://www.tripos.com/data/support/mol2.pdf (see page 12)
Otherwise, for modifing the atom names, I see two options: manually editing
the mol2 file, or doing it with a little script (using babel or not).
Best,
Pascal
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