[gmx-users] CHARMM36 & Gromacs
marianski at fhi-berlin.mpg.de
Thu Aug 17 16:19:40 CEST 2017
Seems like a trivial issue, but google is not helpful here. I intend to
run simulations of (branched) carbohydrates in GROMACS 5.x.x using
CHARMM36 FF (params from
http://mackerell.umaryland.edu/charmm_ff.shtml). In principle, all
building blocks are there, but I have no idea how to generate a topology
file that includes proper glycosidic linkages between the subunits. The
rtp file contains only 'complete' carbohydrates and I don't see any
hints about creating glycosidic bonds (linear or branched).
Any help (preferably some tutorial?) here?
Mateusz Marianski, PhD
email: marianski at fhi-berlin.mpg.de
Faradayweg 4-6, 14195 Berlin, Germany
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