Re: [Open Babel] Option to input net charge and to disable adding protons

[David v. d. S. <sp...@xr...>]

On 2012-10-07 22:53, Reinis Danne wrote:
> On Sun, Oct 07, 2012 at 10:06:57PM +0200, David van der Spoel wrote:
>> On 2012-10-07 21:28, Reinis Danne wrote:
>>> On Sun, Oct 07, 2012 at 08:32:53PM +0200, David van der Spoel wrote:
>>>> On 2012-10-07 18:35, Reinis Danne wrote:
>>>>> On Sun, Oct 07, 2012 at 11:20:16AM +0200, David van der Spoel wrote:
>>>>>>
>>>>>> Related to this it would be great if one could turn off the proton
>>>>>> generation, since for many ions babel adds a proton where there
>>>>>> shouldn't be one (e.g. imidazolium and other ionic liquids, organic
>>>>>> cations).
>>>>>
>>>>> It shouldn't add Hs if there are explicit Hs in the structure
>>>>> already (unless explicitly asked). Do you have a case where it
>>>>> is not so?
>>>>>
>>>> Yes, this happens with gaussian files containing ions (which do have
>>>> info about the formal charge) but not with the corresponding pdb file.
>>>>
>>>> % wget http://folding.bmc.uu.se/1-butyl-3-methylimidazolium-g4.log.gz
>>>> % babel -ig98
>>>> 1-butyl-3-methylimidazolium/1-butyl-3-methylimidazolium-g4.log.gz  -oinchi
>>>> InChI=1S/C8H16N2/c1-3-4-5-10-7-6-9(2)8-10/h6-7H,3-5,8H2,1-2H3
>>>>
>>>> % wget http://folding.bmc.uu.se/1-butyl-3-methylimidazolium.pdb
>>>> % babel -ipdb 1-butyl-3-methylimidazolium.pdb
>>>> InChI=1S/C8H15N2/c1-3-4-5-10-7-6-9(2)8-10/h6-8H,3-5H2,1-2H3/q+1
>>>
>>> Which version of Open Babel are you using? I can't reproduce
>>> this with trunk (which is basically soon to be released 2.3.2).
>>
>> [artemisia:Liquids/DATABASE] % babel -version
>> No output file or format spec!
>> Open Babel 2.3.1 -- Oct  4 2012 -- 19:42:21
>>
>> This is built on a Mac in case that matters, but I get the same on a
>> Linux x86_64 box with a freshly compiled 2.3.1.
>
> Maybe the issue is that it is 2.3.1. Altough I gouldnt find in
> commit log what might have changed to affect this. Could you try
> SVN checkout for 2-3-x branch?
> http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/branches/openbabel-2-3-x/
>
> I guess something like this would fetch it:
> svn co https://openbabel.svn.sourceforge.net/svnroot/openbabel/branches/openbabel-2-3-x
>
>
Unfortunately that doesn't help. I fetched the code and installed it:

% which babel
/Users/spoel/ob23x/bin//babel

[artemisia:~/tmp] % babel -version
No output file or format spec!
Open Babel 2.3.2 -- Oct  8 2012 -- 09:44:21

% babel -ig03 1-butyl-3-methylimidazolium-g4.log.gz -oinchi
InChI=1S/C8H16N2/c1-3-4-5-10-7-6-9(2)8-10/h6-7H,3-5,8H2,1-2H3
1 molecule converted
1 info messages 16 audit log messages

% babel -ipdb 1-butyl-3-methylimidazolium.pdb -oinchi
InChI=1S/C8H15N2/c1-3-4-5-10-7-6-9(2)8-10/h6-8H,3-5H2,1-2H3/q+1
1 molecule converted
14 audit log messages

Other clues?

> Reinis
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
sp...@xr...    http://folding.bmc.uu.se