[AMBER] parameters for metal site

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Thu, 17 Mar 2011 10:24:16 +0100


I am still trying to parametrize the metal site using QM - I have been
able to solve most of the problems but I still have one big problem

In my crystal structure, I have a tetrahedral coordinated metal site
and I would like to observe the changes going to the trigonal state. I
have optimized the complex with QM and get the charges using
Kollman-Mertz schema as described earlier. I use the tutorial from
Ross and build the new residues - thanks to FyD here on the list - I
have made the residues equivalent the three that coordinates the metal
- so I have kept the water molecule which is the fourth coordinating
in the tetrahedral complex and I have kept it in the trigonal to get
some charge transfer of the metal site - I think by removed it the
trigonal structure might be too strongly with respect to binding as
well as charges.

I have parametrized the amino acids ligand as histidine with a new
residue type and the only atom type changes is the coordinating
nitrogen atom - charges have been added in the new lib file. I build
the metal with the water molecule where I have taken the parameters
from TIP3P - the types are the same but the charges are different
which is reasonable in my case. Then I do a minimization of the
complex and the hydrogens go to the negative charges nitrogens on the
histidine residue - so the oxygen of the water has a vdw=1.7682 and
0.1512 and the metal it is 1.74 and 1.14 so the repulsion part so be
rather strong going below 1.5 A but in the minimized complex the
distance is 0.99 between the newly parametrized water and metal and
the hydrogens have a distance between the nitrogens of 0.98 A - so
somehow the vdw does really work for my parameters or libs - I do not
know how to solve this any suggestions or comments appreciated

thanks in advance

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Received on Thu Mar 17 2011 - 02:30:04 PDT
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