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 <div class="gmail_quote">On Thu, Mar 6, 2008 at 9:19 AM, sgiani <<a href="mailto:samuel...@gmail.com">samuel...@gmail.com</a>> wrote: <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> 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 <a href="http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm" target="_blank">http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm</a> 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 <div><div></div><div class="Wj3C7c"> On Mar 5, 8:34 pm, "Jack Shultz" <<a href="mailto:jackyg...@gmail.com">jackyg...@gmail.com</a>> 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 </div></div> </blockquote></div>