Hi, I have the issue in the subject when running obenergy on a Gaussian log file, using obenergy -ff GAFF 123-trimethyl-imidazolium.log > log.out
When I instead use a sdf file there is no problem. obenergy -ff GAFF 123-trimethyl-imidazolium.sdf > sdf.out Both invocations return different atomtypes, correct for sdf and incorrect for Gaussian file. As the message said, no aromatic ring is detected: diff log.out sdf.out | head -n 18 5,9c5,9 < 1 c2 AL < 2 c2 AL < 3 n3 AL < 4 cc AL < 5 n3 AL --- > 1 cd AR > 2 cc AR > 3 na AR > 4 cc AR > 5 na AR 12,13c12,13 < 8 h1 NO < 9 h1 NO --- > 8 h4 NO > 9 h4 NO Suggestions for debugging welcome. -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
123-trimethyl-imidazolium.sdf
Description: chemical/molfile
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