In a previous article, scavetta at XTREME.UCR.EDU ("Robert D Scavetta") wrote:
>I'm trying to refine several Ca+2 binding proteins that have been crystallized
>in the presence of either La+3 or Lu+3. The parameter files for these ions
>give me the following values for eps and sigma (these values were someones
>guess, and not a very good one). I know these are wrong!! Does anyone have
>the correct values or a better guess than what I have??
>>eps (kcal/mol) 0.1000
>eps (1:4) 0.1000
>sigma (A) 1.1500
>sigma (1:4) 1.1500
>>>Thanks in advance for your help.
>>Robert D Scavetta
I am trying to do a similar thing with XPLOR, in refining terbium
ions bound to a protein. A test run using the same non-bonded
parameters as above for La3+/Lu3+ gave reasonable results in terms of
how the Tb3+ are bound by the protein, although it would seem that
the bonding term is much more important for this interaction, esp.
with an ion with a +3 charge interacting with oxygen. From my little
reading, it may be that the Lennard-Jones potential doesn't apply
to many-electron atoms like the ones we are dealing with, and so
these interactions can't be modeled accurately with the Van der
Waals function. Is using the electrostatic function and the CHARge
specification in XPLOR a better way to handle this ? Any comments
would be welcome.
Dept. of Biochemistry
University of Saskatchewan
matte at skyfox.usask.ca