On 2021-05-01 13:02, David van der Spoel wrote:
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.
Some more info: apparently OB needs to know *where* the charge is and
this information is not deduced from the Gaussian log file. There is no
M_CHG field generated, despite the total charge of the compound being
set in the src/gaussformat.cpp code.
Another clue: if the M_CHG field is present but points to the wrong
atom, OB cannot deduce the correct atom types and aromaticity either.
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
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--
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
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