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?
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.
On Thu, Jul 3, 2014 at 9:05 PM, Pascal Muller <pascal.jm.mul...@gmail.com>
wrote:
> 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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