Hello,
It seems that one of the problems related to recognize correct atom types is
the conjugated rings which are not aromatic such as furan ring.
For example, if we use the original gaff.prm file in openbabel for furan, the
atom types are as following.
A T O M T Y P E S
IDX TYPE RING
1 ca AR
2 h4 NO
3 ca AR
4 ha NO
5 ca AR
6 ha NO
7 ca AR
8 h4 NO
9 X AR
As it is shown here, the ring is recognized as an aromatic ring and so the
carbons as “ca”.
However, based on the GAFF force field, C1 and C4 must be “cc” , C2 and C3 must
be “cd”.
Another problem is that oxygen (atom number 9) is not recognized at all.
My question is that which function or routine in the code recognizes aromatic
rings from non-aromatic rings?
Cheers,
Mohammad
> On Jan 20, 2016, at 10:59 AM, Fredrik Wallner <fred...@wallner.nu> wrote:
>
> Hi,
>
> What is the file format of the input structure? Converting from SMILES to
> SMARTS isn’t really necessary since all SMILES are valid SMARTS and can be
> put into the query directly. For other, more advanced queries you could
> always try to convert to SMILES with the options -xn (to suppress name) and
> -xh 1 (to suppress the addition of implicit hydrogens on aromatic nitrogens,
> needs a value i.e. the ”1”, but it can be anything).
>
> Regardless of how you prepare the SMARTS, I can really recommend
> http://smartsview.zbh.uni-hamburg.de to visualize the result to make sure you
> got the correct structure.
>
> Kind regards,
> Fredrik
>> 18 jan. 2016 kl. 16:43 skrev Stefano Forli <fo...@scripps.edu>:
>>
>> Hi Mohammad,
>> when I had to do it myself, I used the CACTVS web service at NIH:
>>
>>
>> http://cactus.nci.nih.gov/chemical/structure/[YOUR-SMILES-HERE]/file?format=smarts
>>
>> Not very straightforward, but you can automate the process using some
>> scripting (bash, python?).
>> Hope this helps,
>>
>> S
>>
>> --
>>
>> Stefano Forli, PhD
>>
>> Assistant Professor of Integrative
>> Structural and Computational Biology,
>> Molecular Graphics Laboratory
>>
>> Dept. of Integrative Structural
>> and Computational Biology, MB-112F
>> The Scripps Research Institute
>> 10550 North Torrey Pines Road
>> La Jolla, CA 92037-1000, USA.
>>
>> tel: +1 (858)784-2055
>> fax: +1 (858)784-2860
>> email: fo...@scripps.edu
>> http://www.scripps.edu/~forli/
>> ________________________________________
>> From: Mohammad Mehdi Ghahremanpour [ghahramanpou...@gmail.com]
>> Sent: Monday, January 18, 2016 6:55 AM
>> To: openbabel-devel@lists.sourceforge.net
>> Subject: [OpenBabel-Devel] Generating SMARTS format
>>
>> Hi,
>>
>> I am updating gaff.prm file by defining new SMARTS format to support all
>> GAFF atom types for different molecules.
>> Is there any routine or function in the code which generates SMARTS from a
>> given molecular structure as the output or even as the stderr?
>>
>>
>> Cheers,
>> Mohammad
>>
>>
>>
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