[gmx-users] CHARMM36 & Gromacs

[Justin Lemkul]

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

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

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