Re: Advice on heteroatoms, metals and water

[Jim Procter <>]

Karsten wrote :
> Thank you for this information. In fact, I was hoping that Modeller had
> some forcefields hidden somewhere in the depth of its code to do loop
> modelling around  Ca2+ binding sites. The real problem is not to place the

no such luck - it uses a reduced version of amber without the bells and 
whistles (FFT/QMM electrostatics, etc).

> Ca2+, but to have all the oxygens of the different side chains point its
> way. My templates are not close enough to get this right, and I have even
> one case where the Ca-binding site is only present in the target.

Well. Without good homologs for the metal binding site, which means that the 
local environment of the loop is roughly similar too, you will have a hard 
time applying any kind of homology modelling procedure reliably. Particularly 
so, if you want to use this for molecular replacement. This is because 
MODELLER uses a knowledge-based algorithm to generate the constraints, and is 
not necesarily going to be able to predict something it hasn't seen before 
(ie in the loop-database used in the loop-modelling procedure).

The only 'reliable' approach is to find an ab-initio geometry for the loop, 
which you might get using a good dynamics package. Amber is perhaps 
appropriate (IIRC) if you use the proper electrostatics, but there are other 
packages out there. Either way, you will need a cautious combination of 
simulation and homology modelling in order to get anywhere. The complex issue 
of setting restraints on the overall fold of the molecule is unavoidable, I'm 
afraid.

However, if you just want to make a nice picture using the text-book 
coordination geometry, you could try adding some appropriate distance and 
dihedral restraints to your model - have a look here :
http://salilab.org/modeller/manual/node113.html

have fun ;-)
j.