Hi,
On Fri, Jan 14, 2011 at 04:27:53PM -0500, Geoffrey Hutchison wrote:
> > Browsing openbabel-2.3.0/src/charges seems to confirm that
> > 'none' is not a charge option.
> > Is there another way to ignore the charges ?
>
> At the moment, not from the user utilities, no. I just added a "none" option
> to the development trunk.
thanks.
> > 'input_file' - use the charges already in the input file -
> > would also be very useful.
>
> Except if you don't specify the --partialcharge flag, this is exactly what
> happens. So I don't see how this is all that useful.
If the charges in the input file are all zero then the output file
will contain nonzero gasteiger partialcharges. An 'input_file' option
would be useful for batch processing, e.g.: some of the files to be
processed have nonzero charges and some have all zero charges.
In this case option 'none' would lose the preexisting nonzero charges.
In addition, babel's current behavior does not emit a message
indicating what type of charges are being output. Admittedly,
one can read the documentation, but i would have found a message helpful.
% babel -i mol2 r.mol2 -o pdbqt r.pdbqt
1 molecule converted
582 audit log messages
% head r.mol2
@<TRIPOS>MOLECULE
allatom_refine_001.pdb_0
43 44 1 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 0.9889 0.2571 -8.4831 C.1 1 UNK1 0.0000
2 C2 -0.2284 -0.5009 -6.5158 C.ar 1 UNK1 0.0000
... 0.0000
% head r.pdbqt
USER x y z vdW Elec q
Type
USER _______ _______ _______ _____ _____ ______
____
ROOT
HETATM 1 C14 UNK A 1 -0.230 -1.671 -2.318 0.00 0.00 +0.250 C
HETATM 2 N2 UNK A 1 0.877 -1.274 -3.060 0.00 0.00 -0.283 N
> > Finally, the documentation should be improved to describe the
> > valid <method>'s:
>
> Try "babel -L charges"
Ahhh, ok now i see the light at the tail of babel -H
thanks,
scott
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