[gmx-users] Chitosan topology
tsjerkw at gmail.com
Wed Aug 1 09:05:26 CEST 2007
Note that parameterization of compounds is not for the faint of heart
(http://wiki.gromacs.org/index.php/Parameterization). For chitosan,
you first want to get the parameters for one building block right. In
case you want to use the GROMOS force field, search papers of Roberto
Lins, who parameterized the sugars for the GROMOS 45a3 force field.
Then go for di- and tri-glycans and be sure that these give reasonable
behaviour. If that works, you can go for the larger ones, ideally
writing a .rtp building block CTS and contributing it on the gromacs
contributions site :)
Note also that I'm conveniently neglecting any work you presumably did
w.r.t. parameterization, assuming that you didn't do it in a correct
manner, since you mention you get (otherwise unspecified) poor
results. If you think I'm too harsh on you, you should really consider
taking Yang Ye's advice and give more information about the things you
did and the nature of your poor results.
On 7/31/07, Yang Ye <leafyoung at yahoo.com> wrote:
> Please describe clearly your "poor results".
> Yang Ye
> On 7/31/2007 10:55 PM, Antonello wrote:
> > Dear gromacs users,
> > i apply to your kind attention to know if someone have already parametrized the
> > chitosan structure.
> > I am trying to do it but with poor results.
> > Can you help me?
> > Thanking in advance
> > Dipartimento di Medicina Sperimentale
> > Universita' degli Studi di Parma
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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