[gmx-users] Re: Amber 2 gmx

[Anton Feenstra]

Patrick Ladam wrote:
> 
> Anton Feenstra wrote:
> 
> > Patrick Ladam wrote:
> > >
> > > Hello Anton,
> > >
> > > I am trying to get GMX do some MD upon a 20mer DNA. It works excepted I can't
> > > get the hydrogens to be considered correctly (they spread away as soon as I do a simple
> > > minimisation). I tried different FF with no success. Actually I use NMR distance restraints
> > > and I really need these hydrogens. Did you do such calculations successfully?
> >
> > I don't see what you mean exactly when you say 'hydrogens considered correctly'.
> 
> More precisely  bonds are not built with their heavy atoms, they just spread away
> when running a simple minimisation. Since my last mail I understood that these
> hydrogens are simply not present in any FF (not in ffgmx nor ffgmx2) so I have no
> solution than to build the FF myself which I don't really feel confident in doing...

Actually, ffgmx2 *was* made precisely for this type of simulations,
and it *does* contain *all* hydrogen atoms, also the aliphatic (CH,
CH2, CH3) ones. I am surprised that it does not work. But then, are
the nucleo-bases (DNA) in the ffgmx2 - probably not...?

Adding hydrogens should not really be too much of a problem. For most
of them, you only need a single bond and an angle or two. Some would
also require a proper or improper dihedral. And you might need to add
some default parameters, or specify the parameters explicitly or using
a #define (as done in the Gromos - ffG43 - forcefields). After this,
you should even be able to dummify them using the pdb2gmx -dummy option.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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|  \__/  | "Uh-oh .... Right Again" (Laurie Anderson)                |
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