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

Yun Shi yunshi09 at gmail.com
Sun Aug 7 21:05:44 CEST 2011

Thanks again.

Since I am running MD simulation on a public cluster, I cannot modify
atomtypes.atp and ffnonbonded.itp on that cluster.

But I could get every parameter ready and prepare the xxx.tpr files locally,
and pass them to the cluster. So the practical question is, does the tpr
file contain all those C12 and C6 LJ parameters already? Or mdrun need to
retrieve these parameters according to the atom types from corresponding
files within the gromos53a6.ff folder?


Yun Shi

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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