Tsjerk
On 3/29/06, Hugo Verli <[EMAIL PROTECTED]> wrote:
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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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