Le 11/09/2025 à 09:04, FyD via AMBER a écrit :
>
> laptop:~/Work/P9709/> grep -En "c3-c3-c -o|o -c -c3-c3"
> /usr/local/amber24/dat/leap/parm/gaff211.dat
> 7360:o -c -c3-c3 1 0.270 180.000 2 p14 SS
> AUE=0.2361 RMSE=0.3321 TorType=3
> 7409:c3-c3-c -o 1 0.030 180.000 -2
> sialic1,t37,t41 GA AUE=0.7374 RMSE=0.9897 TorType=3
> 7410:c3-c3-c -o 1 0.550 180.000 -3
> 7411:c3-c3-c -o 1 0.740 0.000 1
Dear all, dear François (and happy New Year),
Taken alone, I would consider lines 7409, 7410 and 7411 for complement
themselves to have since phase and dihedral angles are not identical,
so they *could* be in this scheme to have a more complex potential (I
have probably an old gnuplot script somewhere to show this).
For the comparison of lines 7360 and 7409 (phase is reversed) i do not
know if they add or if only one of the dihedral is picked
depending on the situation (i.e. atom order matters).
Out of curiosity, do you have sample molecules where these circumstances
appear?
That would probably allow to determine how the codes handles these
scenarios (and thus if this is intended, expected, or a bug).
HTH,
Stéphane
--
Maître de conférences Hors Classe, PEDR, HDR
US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics, F-44000 Nantes
http://www.us2b.univ-nantes.fr/ - http://www.steletch.org
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Received on Fri Jan 09 2026 - 01:00:02 PST
