RES: [gmx-users] gromacs with carbohydrates

[Hugo Verli]

Dear Andreas,

As David mentioned, I think that prodrg is the best way to represent
carbohydrates in GROMACS. I have simulated heparin and other carbohydrates
(sulfated or not) both in solution and complexed with proteins, and had
obtained a high level of accuracy with experimental data, as NMR, X-ray and
mutagenesis. The results are fine both with GROMACS force field and with
GROMOS96 force field.

I only suggest a special attention to carbohydrate ring conformation. If it
distort during the simulation I suggest that you fix it in the expected
conformation by using improper dihedrals. 

Best regards,

Hugo Verli.

-----Mensagem original-----
De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Em
nome de David van der Spoel
Enviada em: quarta-feira, 29 de março de 2006 10:10
Para: Discussion list for GROMACS users
Assunto: Re: [gmx-users] gromacs with carbohydrates

Andreas Steffen wrote:
> hi,
> is there an adequate forcefield in gromacs for dealing with
> carbohydrates (cyclodextrin) or do I have to map the atoms to the
> protein atom types?
> Thanks in advance!
> Andreas.
> 
try starting with prodrg

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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