[gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 7 20:39:28 CEST 2011

Yun Shi wrote:
> Hi Justin,
> Thanks a lot for the replies.
> I wonder what are the "newer versions" you indicated, but I find one as:
>   /A reoptimized GROMOS force field for hexopyranose-based carbohydrates
>   accounting for the relative free energies of ring conformers, anomers,
>   epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/
> . This new version 56A_CARBO   is claimed to be "nearly equivalent to 
> 53A6 for non-carbohydrate systems", and I find, at least, atomic charges 
> for C1 and C5 look more chemically reasonable.
> But changes for a couple of 1-4 van der Waals parameter C12 were made to 
> 53a6 force field, and additional atom types were added. So could you 
> tell me which file contain those LJ parameters with respect to different 
> atom types?

New atom types need to be added to atomtypes.atp and their parameters defined in 

> Alternatively, would it be reasonably good enough to use your 
> Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate 
> molecules by PRODRG, and then modify the atomic charges according to the 
> 56A_CARBO paper?

Maybe, but check the bonded parameters carefully.  Sugars are particularly 
sensitive to incorrect angle and dihedral parameters, especially.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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