Re: [Pdb2pqr-users] error when using pdb2pqr: KeyError: 'PEOE Error: Atomtype <S.O2> not known

[Francois B. <ber...@ri...>]

My colleague Dr. Arnout Voet has a patch correcting this.
It is attached to this e-mail.

On 07/17/2012 02:32 PM, Francois Berenger wrote:
> Hi,
>
> Should I be worried about this:
>
> cd crash_0000001; /usr/local/pdb2pqr/pdb2pqr.py --ligand=0000001.mol2
> --ff=AMBER --chain --whitespace ../prot-receptor.pdb 0000001.pqr
>
> Traceback (most recent call last):
>     File "/usr/local/pdb2pqr/pdb2pqr.py", line 65, in <module>
>       mainCommand(sys.argv)
>     File "/usr/local/pdb2pqr/main.py", line 619, in mainCommand
>       ffout = options.ffout)
>     File "/usr/local/pdb2pqr/main.py", line 330, in runPDB2PQR
>       Lig.make_up2date(residue)
>     File "/usr/local/pdb2pqr/pdb2pka/ligandclean/ligff.py", line 272, in
> make_up2date
>       self.recalc_charges(residue)
>     File "/usr/local/pdb2pqr/pdb2pka/ligandclean/ligff.py", line 362, in
> recalc_charges
>       calc_charges(residue)
>     File "/usr/local/pdb2pqr/pdb2pka/ligandclean/peoe_PDB2PQR.py", line
> 88, in PEOE
>       raise KeyError, 'PEOE Error: Atomtype <%s> not known, treating atom
> %s as dummy' % (a.sybylType, a.name)
> KeyError: 'PEOE Error: Atomtype <S.O2> not known, treating atom S18 as
> dummy'
>
> Thanks,
> F.
>
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