Parameters

[sgiani]

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