[gmx-users] Re: Amber 2 gmx

[Anton Feenstra]

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'.
For starters, which hydrogens are you talking about? Just the polar ones
(which are in all of the ff's), or also aromatic (in some of the ff's) or
aliphatic ones (only in ffgmx2)? If you need only a limited number of hydrogen
positions, you could introduce them as dummy atom constructions manually
(like it is automatically done with the -dummy option of pdb2gmx, except that
those replace 'real' force-field defined hydrogens).

> I have found in the mail-list you wrote scripts to convert Amber FF to GMX and would be
> interested in trying this but maybe this is just beta work and not yet available?

THis is absolutely not in any working order. It is now in a stage that
output files are generated, which can even be used to generate a starting
file (.tpr) for mdrun, but the forcefield is not completely converted, 
some important items are still missing so the resulting simulations will
be quite useless, I'm afraid. Unfortunately I have ran out of time for this
work, but other people seemed very interested and I heard that there is
still work going on on this. So I suggest you stay tuned to the lists to
see if new developments are appearing.


[P.S. sorry for the cross-post, but this is both user- and developer-
related info...]

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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|  \__/  | "The Stingrays Must Be Fat This Year" (Red Hot Chili      |
|        | Peppers)                                                  |
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