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

Yun Shi yunshi09 at gmail.com
Sun Aug 7 20:36:18 CEST 2011

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 56ACARBO  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?

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 56ACARBO paper?


Yun Shi

Yun Shi wrote:
> Hi all,
> I am doing MD simulation of some carbohydrate-protein complex with this
> 53a6 force-field.
> I noted that in any oligosaccharide, the charge assigned for anomeric
> carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is
> 0.376. This is kind of counter-intuitive for me since the anomeric
> carbon C1 is linked to two oxygen atoms O5 and "O1" while C5 is linked
> to only one oxygen atom O5, and both C1 and C5 are CH type atom. And in
> other force filed like GLYCAM06, C1 always has a larger positive partial
> charge than C5.
> I understand that GROMOS force fields are derived in quite different
> ways, but I still wonder if it makes sense to switch the charges on C1
> and C5?

No, but the charges used may not be the best ones anyway.  There are newer
revisions of 53A6 that are much better.

> It seems these carbohydrate parameters did not change in the new 54a7
> ff, which was tested against nOe and J-coupling data rather than free
> enthalpy of hydration and solvation, which really puzzles me.

54A7 was principally a revision of protein atom types and one lipid type;
nothing in the sugar parameters was modified.



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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