[gmx-users] CHARMM36 & Gromacs

Justin Lemkul jalemkul at vt.edu
Fri Aug 18 19:01:05 CEST 2017

On 8/17/17 10:18 AM, Mateusz Marianski wrote:
> 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?

You'll have to go into the actual CHARMM force field files (specifically 
top_all36_carb.rtf) and look for the patches that will be used to link 
the monomers (PRES entries).  Those specify changes to atom types and 
charges.  Then you'll need to construct a new .rtp file for the entire 
carbohydrate.  GROMACS is not very good at doing things that are 
branched.  You can try to employ specbond.dat but I suspect that will 
fail given the extent of changes that have to be made.

The other alternative is to use CHARMM-GUI to prepare a topology. As 
long as your residue and atom names are CHARMM-compliant, it should 
generate the system (even files in GROMACS format) just fine.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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