[gmx-users] Re:Re: x2top

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 28 20:59:37 CET 2008


> if i just use the topology of the sugar without the protein then the
> simulations starts but the atoms are not moving during the simulation. they
> are exactly at the same position in frame 1 and frame n. therefore had the
> idea to use the build-in x2top function. so i would be glad to get it
> somehow working...

Well, I don't see how a topology from x2top would do different than
one from PRODRG or one generated properly. PRODRG doesn't write
position restraints. Did you happen to have integrator set to steep in
the .mdp file?

I get the impression that you first have to come to terms with Gromacs
and performing simulations, before trying to do the combination
protein/sugar. But that may just be me.


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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