[CP2K:735] Re: Parameters

[Jack Shultz]

Thanks.
I'm interested in a Iron Sulfur cofactor for Fe-Hydrogenase, it is called
the H-Cluster. There are several papers characterizing the structure and
deprotonization reactions it can catalyze. I'll looking into empirically
parametrizing. Thanks for the tip.

Jack

On Thu, Mar 6, 2008 at 9:19 AM, sgiani <samuel... at gmail.com> wrote:

>
> Hi Jack!
>
> you didn't mentioned the system you would like to investigate, but
> since you have planned to use xleap, I assume you are dealing with
> biopolymers and/or organic molecules. For the first case you should
> have all the force fields already available, while for the second case
> usually the general atoms force field "gaff" is available in the amber
> package. The case is usually more complicated if you have to consider
> transition metals.
>
> For missing parameters, amber has built-in tools to empirically
> parametrize, it is also smart enough to try and find out similarities
> between the type of atoms you have and the ones presents in the force
> fields. Have a look at
> http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm
>
> You can try
>
> $AMBERHOME/exe/parmchk -i foo.prepin -f prepi -o foo.frcmod
>
> If this doesn't solve the problem you should consider a survey in the
> literature harvesting parameters or a complete individualized
> parametrization for your molecule of interest.
>
> Ciao, Samuele
>
> On Mar 5, 8:34 pm, "Jack Shultz" <jackyg... at gmail.com> wrote:
> > How do researchers generally obtain parameters for bond distances and
> > energy? Reason is, I am playing with xleap and the parameter files do
> not
> > have data on several bonds. In some situations I was able to look up
> > empirical data on bond distance and bond energy to make the appication
> > happy. Would the CRC handbook be an approriate reference?
> >
> > Jack
> >
>
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