[gmx-users] Carbohydrate force fields in GROMACS

[mish]

Many thanks.  I know parameters are available in literature but my question
was how to use them in GROMACS. Now, I can see different residue names
(e.g  AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM).
I think I will need to edit input pdb file accordingly. However, I am still
not sure of methylated monosaccharides have to be constructed as "modified
monosaccharides", or there are CHARMM parameters for methy (as  a separate
residue) available and one should use 2 residues in such case. I will have
a look in archive to find-out how to create  modified monosaccharides.

Many thanks,
Mish

On Fri, Mar 20, 2015 at 5:00 PM, Marcelo Depólo <marcelodepolo at gmail.com>
wrote:

> There is also a Modified GROMOS forcefield for glycans here:
>
> http://dx.doi.org/10.1021/ct300479h
>
> Cheers!
> --
> Marcelo Depólo Polêto
> Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
> B.Sc. Biochemistry - University of Viçosa (Brazil)
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