Atomic charges parameters

The solvent dielectric constant, ionic strength and temperature are chosen to fit the conditions of the experimental studies. The protein dielectric constant is assigned some small value, e.g. 4. The PB calculations are currently carried out with the atomic charges and radii of the PARSE parameter set, developed by Honig and coworkers [17] or that for CHARMM [12]. The PARSE parameter set... 

If the MM+ option to n sc bond dipoles for nonbonded electrostatic calculation s is set, then MM-t-ignores atomic charges but uses dipole m om en ts supplied in its parameter set (in themmpstr. files ). 

The presence of the q B term with its implied distance dependency means that the charges depend upon the molecular geometry. Thus, should the conformation of a molecule change the atomic charges will also change. Just three parameters are required for each atom in the system (the electronegativity, the idempotential and the covalent radius). 

Assign atom types Assign connectivity Assign partial atomic charges -------Assigninitiai-parameters. "... 

Starting geometry 4A) External parameters [—> Parital atomic charges... 

All properties (energy, dipole moment, atomic charges) and geometry parameters (distance, angle, dihedral angle) can be animated or stepped through. 

One of the more difficult decisions to be made is the proper value for the Lennard-Jones parameters. These relate to the interaction between the quantum mechanical atoms and the MM atoms. At the time of writing (1999), there does not appear to be a consensus amongst researchers. Some authors recommend a 10% scaling of the traditional 12-6 parameters. Some authors scale the MM atom charges. 

Another problem of atomic charges determined by fitting is related to the absolute accuracy. Although inclusion of charges on all atoms does not significantly improve the results over those determined from a reduced set of parameters, the absolute deviation between the true and fitted electrostatic potentials can be quite large. Interaction... 

An error function depending on parameters. Only minima are of interest, and the global minimum is usually (but not always) desired. This may for example be determination of parameters in a force field, a set of atomic charges, or a set of localized Molecular Orbitals. 

Energies are in kcal/mol, distances in A, and atomic charges in au. Parameters not listed in the table are the same as in previous chapters. 

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