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

[Justin A. Lemkul]

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 
ffnonbonded.itp.

> 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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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