RES: [gmx-users] Re: large carbohydrates

[Hugo Verli]

Dear Peter,

When using PRODRG to simulate carbohydrates you may have problems to
describe the monosaccharide conformations, but it’s a system dependent
problem. Considering usual carbohydrates, founded in biological glycosylated
proteins, the chair conformation is adequately described (the chair-chair
interconversion occurs in time scales far than usual simulations), with no
occurrence of twist-boat conformations. If you have some unusual ring
conformation, as the iduronic acid in heparin, you can fix the conformation
with improper dihedrals and correctly describe the glycosidic linkage
geometry, even in complex and highly charged polysaccharides. Such
proceeding also makes possible to determine the specific energetic
contribution of each monosaccharide conformation upon complexation to target
proteins.

One possible problem that you may find is the limited variety of
carbohydrate substitution patterns in GROMOS parameterization. Several
monosaccharides frequently founded in biological proteins are not included
in the force field, so you will need to build your own parameters. It also
works fine and, at least for the global geometry of the carbohydrate moiety,
you will be capable to reproduce experimental geometry even with a certain
level of variation in atomic charges.

Best regards,

Hugo Verli.

-----Mensagem original-----
De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Em
nome de Vojtech Spiwok
Enviada em: segunda-feira, 15 de maio de 2006 12:30
Para: gmx-users at gromacs.org
Assunto: [gmx-users] Re: large carbohydrates

Dear Peter

Unfortunately, carbohydrates require special
parametrization of torsions and therefore you
should not use PRODRG topologies.

Vojtech Spiwok
ICT Prague

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