Hi,
APBS's requirement is that the atom should have different names, unless you
> want it to ignore the duplications.
>
> I can see that Babel adds number behind heavy atoms like C, O, etc. Why
> doesn't it do so to H?
>
> I don't know.
> After searching for mol2 format of AB1, I have found this:
>
> http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=PDB_AB1
>
> I haven't checked the files yet, but my purpose is solving the potential
> of ligand on each PDB, therefore I can't use this.
>
>
And what's your definition of "ligand" in the PDB? :)
Anyway, if you don't want to write a script to modify H atom names (should
be easy), you may use a text editor (e.g. vi, two steps, if molecule names
don't have double H), or automatise the mol2 download (if you have the HET
code list) - but you still may not be sure that the bond types are correct,
unless specified otherwise on the website...
Regards,
Pascal
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