[gmx-users] CHARMM36 & Gromacs

Mateusz Marianski marianski at fhi-berlin.mpg.de
Thu Aug 17 16:19:40 CEST 2017

Dear All,

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
phone:               +49-30-8413-5623
der Max-Planck-Gesellschaft
Faradayweg 4-6, 14195 Berlin, Germany

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