On 20/01/16 10:59, Fredrik Wallner 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. > Thanks for the tip!
The issue at hand is to debug GAFF atomtype generation and therefore to see which SMARTS match the atomtype. To do this we have added a print statement to forcefieldGAFF.cpp that shows how the program cycles over the list of smarts in gaff.prm until it converges, e.g. using a Gaussian log file as input: % obenergy -ff GAFF pyridine.log Atom X-1 smart [*] Atom X-2 smart [*] Atom X-3 smart [*] Atom X-4 smart [*] Atom X-5 smart [*] Atom X-6 smart [*] Atom X-7 smart [*] Atom X-8 smart [*] Atom X-9 smart [*] Atom X-10 smart [*] Atom X-11 smart [*] Atom ha-2 smart [#1X1] Atom ha-4 smart [#1X1] Atom ha-6 smart [#1X1] Atom ha-8 smart [#1X1] Atom ha-10 smart [#1X1] Atom hc-4 smart [#1X1][CX4] Atom c3-3 smart [#6X4] Atom c2-1 smart [#6X3] Atom c2-5 smart [#6X3] Atom c2-7 smart [#6X3] Atom c2-9 smart [#6X3] Atom cc-7 smart [#6X3;R](=*)-*=* Atom cc-9 smart [#6X3;R](=*)-*=* Atom n2-11 smart [#7X2] Atom n1-11 smart [#7X2](=*)=* Atom n1-11 smart [#7X2](=*)=* > 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 >> >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. 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Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> _______________________________________________ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. 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