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

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 7 05:27:51 CEST 2011

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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