[gmx-users] x2top

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 27 22:07:44 CET 2008

Hi Bernhard,

>> I tried to use the x2top function of gromacs 4 on a sugar-molecule.

>> Library file ffG43a1.n2t not found in current dir nor in default

Why would you want to use the Gromos96 43a1 force field for this and
why use x2top to provide the topology for it? As Justin said, you
could use the PRODRG topology. But carbohydrates have been properly
parameterized for the Gromos96 45a3 force field (and the parameters
are als in 53a5/53a6). If you're serious about the dynamics of your
sugars, you'd better construct a topology in line with these
parameters. For the parameters, check the paper from Roberto Lins and
Wilfred van Gunsteren (don't know the ref by heart).



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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