Hi,
I am trying to calculate partial charges for Zinc in the cat site of an enzyme. The crystal structure shows a zinc ion with a coordination of three HIS residues, with zinc held in place by the =N- atoms on the side chain. I have seen this work before, but only on the cat site of this particular enzyme. I am trying to do the whole thing enzyme. So rather than just two zinc ions, I want to calculate partial charges for 2 zinc ions and 6 calcium ions. The charges would then be used to parameterise the Ambersb FF.
So I understand how to use RED server, and I know how to apply a restraint on the charge with capped groups to make intermediates with a net charge of 0., etc..
The issue I am having is with the actual Gaussian ab initio (in my case RED uses hf/6-31g(d)) optimisation. After charges have been assigned, I look at the output and the structure is very different to the crystal structure. To the point where one HIS residue is now orientated in the opposite direction from the zinc ion.
So looking at the earlier published work, I tried optimising things myself (using hf/lanl2dz - same as in the published work). I still don't get a good coordination of HIS with ZINC. Thus, I am reluctant to upload the .log fie to RED until I am happy with the optimised geometry.
Please people, any advice would be very grateful.
Many thanks
Anthony
You may try a partial optimization using popt or ReadOptimize in Guassian.
Those options will not balance the charges for the Amber force field. They won't apply legrangian multipliers on the capped ends of the peptide backbone to 0.
Well, without any restriant it is obvious that upon optimization the crystal structure geometry will not be preserved. In order to get correct charges for the geometrical arrangement of Zn/Ca present in the active site of your enzyme, you need to derive partial charges in a conformational arrangement similar to crystal structure of your enzyme. Is'nt that?
Then you may try some relaxed criteria for geometry optimization available in RED server, such as ON2 (normal geometry optimization), rather than tight optimization which is default in RED
.
Net atomic charges, also called partial charges or partial atomic charges, are commonly used for two different purposes: (1) to quantify the transfer of electrons between atoms in a material as computed by quantum chemistry and (2) to construct force-fields (for classical molecular dynamics or Monte Carlo simulations) that approximately reproduce the electrostatic potential surrounding the material. While quantum chemical topology (QCT), also called quantum theory of atoms in molecules (QTAIM), often describes electron transfer in buried atoms with reasonable accuracy, the QCT atomic charges are not suitable to construct point-charge models for classical force-fields, because the QCT atomic multipoles are large in magnitude. (The QCT method can be used to construct accurate force-fields using multi-centered polyatomic multipole expansions, but these are more complicated than the simple point-charge based force-fields often used.) On the other hand, electrostatic potential derived point charges (e.g., CHELP, CHELPG, ESP, Merz-Singh-Kollman, REPEAT) have reasonable accuracy for reproducing the electrostatic potential surrounding the material, but these do not accurately describe electron transfer for buried atoms.
The density –derived electrostatic and chemical (DDEC) methods solve this problem by partitioning the electron density to simultaneously reproduce atomic chemical states and the electrostatic potential surrounding the material with excellent accuracy. The latest generation (called DDEC6) is described in these papers: (a) T. A. Manz and N. Gabaldon Limas, “Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology,” RSC Advances, 6 (2016) 47771-47801 (http://dx.doi.org/10.1039/C6RA04656H) and (b) N. Gabaldon Limas and T. A. Manz, “Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials,” RSC Advances, 6 (2016) 45727-45747 (http://dx.doi.org/10.1039/C6RA05507A). It gives net atomic charges that are closely correlated to many experimental properties as described in those articles. The DDEC6 method is implemented in the free Chargemol program (http://ddec.sourceforge.net) which can analyze results of GAUSSIAN, VASP, and other quantum chemistry programs.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics