Re: any volunteer for packaging "reduce" ?

[Steffen Möller <steffen_moeller@gmx.de>]

On 09/04/2011 04:19 PM, Michael Banck wrote:
> Hi,
> 
> On Sun, Sep 04, 2011 at 12:23:04PM +0200, Steffen Möller wrote:
>> This is a bit more for debichem or debian-science, but mentioned
>> in the autodock tips'n'tricks documentation. Well, just any volunteer
>> for packaging
>> 	http://kinemage.biochem.duke.edu/software/reduce.php
>> would be most welcome.
>>
>> The package is free in some GNU sense but has a custom 5-10 lines
>> license. The source code needs some clean up from .a and .o files,
>> and it comprises at least one library libpdb that may be investigated
>> to appear as a separate binary package.
>>
>> I do not have the time for it but happily serve as a mentor/sponsor.
> 
> I might take a look at some point, but note that openbabel can likely do
> it as well:
> 
> obabel -h -ipdb input.pdb -opdb input_with_h.pdb
> 
> The -h switch adds hydrogens.

Another tool to mention in this context that we already have in our
distribution is pdb2pqr
	http://www.poissonboltzmann.org/pdb2pqr/
This paper
	http://www.chemcomp.com/journal/proton.htm
gives a neat overview ... and motivation to use their method "Protonate 3D"
which is apparently not freely available.

Of interest for the receptor side (and us) would be the GPLed ProtoFit
	http://protofit.sourceforge.net/protofit_download.html
but I would leave it to someone more active in the field to judge preferences
here.

Many thanks and greetings

Steffen