Parameterization of force field Campos de fuerza

1. 1
Parameterization of Force-Field
Jose Luis Guayllas Sarango1
1
Escuela Superior Politecnica de Chimborazo
1
physics@hotmail.es
Abstract-A procedure for the parametrization ie classical molecular mechanics which are based on the same force fields which
in turn is determined at atomic level without considering motion of electrons occurs. The parameterization can be in terms of
binding and non-binding terms depending on the software that will be used which take different parameters in order to adjust the
model to simulate the posterior want to try to get results commensurate with their configuration (parameterization). This paper
describes the parameterization and softwares as AMBER and CHARM used.
Index Terms—Parameterization,Force Field, AMBER, CHARM.
I. INTRODUCTION
Force-field parameter refers to ways of taking certain
Avalues or keep them constant values for the calculation is
not necessary to take them into account. A parameter is
nothing but a fact that is taken as needed to analyze or
evaluate a situation. From the parameter, a given
circumstance can be understood or placed in perspective.[1,2]
The determination of the parameters of the force field is the
key step in the development of a force-field. The current force
fields have been carefully parameterized using experimental
data and quantum calculations on model used as reference
systems. This ensures the quality of later classical calculations
and its ability to reproduce the experimental values. There are
many fields of frames developed forces with different
application, that is, that have been designed to treat various
molecular systems. You can find force fields to study poly
peptides and proteins, nucleic acids others to study, to study
other small organic compounds, etc..[3]
In this w ork, dif ferent parameters that use the sof tw are as
AMBER and CHARM are essent ially useful for describing the force
f ields corresponding to link or not link terms of the Molecular
Mechanics is based on classical terms are explained.
II. WHAT IS PARAMETERIZATION
To know that is a parameterization can start with defining
Configuring, which can also cover many concepts from differ-ent
points of view as: Math, statistics, chemistry, which have a
concept according to its nature so we will try to define a formal
way. It refers to the possibility that the implementation allows
modifying specific aspects of their funcionamiento.Debido to
accounting systems this possibility is more limited than in the
general purpose, the user must not acquire applications that
include incompatible with rigidities their needs. In the case of
custom applications, the user must decide on significant issues
i n the design of the software (AMBER), (CHARM). [4,5]
Much of the functionality of the system is based on a
set of values that directly affect their behavior, why then
Manuscript received July 2, 2014; revised July 9, 2014. Corresponding
author: Jose´ Luis Guayllas Sarango (email: physics@hotmail.es.
personalization should proceed with the configuration of
the system, once the implanter known customer process
proceeds to configure the system for it to adapt as much
as possible, processes and customer requirements.
III. FORCE-FIELD
The force field In the classical methods the Hamiltonian is
expressed by simple equations that depend on the nuclear
positions forming the force field. This can be defined as the
empirical potential energy dependency relative to the geometry
of the core, where the impact of the electrons is implicitly
entered using a set of parameters . These effective potential
allows to study large systems provided there is no disruption of
covalent bonds or drastic changes in the electronic distribution.
For nucleic acids, the most widely used force fields are
AMBER (28) and CHARMM (29), which have been able to
replicate structures and macroscopic properties such as recent
reviews of the field (10, 30 are shown, 32). According to the
data, the best results for the study of canonical and unusual
forms of nucleic acids obtained with the AMBER force field
(33-35), which has been used in this work.[6]
IV. PARAMETERIZATION FORCE-FIELD
The force field over assign functionality gives characteristic
parameters for each type of atom. A force field include various
parameters for the oxygen atom of carbonyl and hydroxyl.
The parameter set includes values for atomic mass, van der
Waals radius and partial charge of individual atoms, also
equilibrium values of bond lengths, angles and dihedral angles
of pairs, triplets, quadruplets and bonded atoms, but the
values corresponding to the effective spring constant for each
potential.[7] Mos t current force fields us e a ”fixed charge”
which assigns each atom a single value for the atomic charge
is not affected by the local electrostatic environment, proposed
developments in force fields are the next generation of models
incorporating polarizable in which the charge of a particle is
influenced by electrostatic interactions with its neighbors. For
example, the polarizability can be approximated by introducing
induced dipoles, or may also be represented by

2. Drude particles, or without mass-load they carry, virtual points
connected by harmonic oscillator potential to each polarizable
atom. The introduction of the polarizability in a force field has
been inhibited by the high associated computational cost when
it comes to calculating the local electrostatic field.[8] Although
many molecular simulations of biological systems involving
macromolecules such as proteins, DNA and RNA, the
parameters for a given type of atom are generally derived from
observations on small organic molecules that are more
amenable to experimental studies and quantum calculations.
The different fields of force may be derived from different types
of experimental data, such as the enthalpy of vaporiza-tion
(Optimized Potential for Liquid 40 Simulations (OPLS)),
sublimation enthalpy, dipole moments, or several parameters
Spectroscopic.
May be experimental or theoretical thereof who are
involved under the terms of bond and non-bond terms
as the group to which these relate.
A. Terms bonding
Also know n as exper imental parameterization, it is custom-ary
to use data f rom IR, Raman, NMR, X-ray or neutron dif f raction. In
terms of torque is common to use a quantum parameter ization
because of the absence of experimental data.
B. Terms nonbonding
They are also considered as a theoretical
parameterization in which you can find as the electrostatic
energy, the energy of Van der Waals and solvent.
1) The electrostatic energy
Partial loads are obtained from a quantum parameterization.
In early versions of the AMBER force field ESP method, which
consists in adjusting the quantum electrostatic potential
determined in a set of points around the molecule was used.
However, inaccurate levels of quantum calculation (HF/STO-
3G), which gave poor results, particularly nucleic acids sub-sequent
versions calculation HF/6-31G (d) were used as refer-ence
is used, it tends to overestimate the dipole moments and
thus simulating the polarizing effect of the water. In parallel,
the RESP methodology is introduced to solve certain devia-tions
present in loads of buried atoms. In most current AMBER
(2002) settings, very high levels of calculation (B3LYP/cc-pVTZ)
with multicentric load representations incorporating
permanent polarization effect, in addition to introducing the
induced polarization are used. These force fields have not yet
been widely applied to the study of nucleic acids.[9]
2) The van der Waals energy
The parameters can be obtained both quantum
mechan-ical and experimental data. Theoretically you
should get for each different pai r of atoms. However, the
combinatory rules Lorentz-Berthelot, where the collision
diameter exits the arithmetic mean and the well depth of
t he geometric mean to apply the atoms interactional.
3) The solvent
In the simulations performed water occurs explicitly models
using TIP3P and SPC. This shows that the water molecule is
rigid loads empirically derived and is considered a single
2
point of van der Waals interaction. Though these models
are simple detailing accuracy conclude that the
properties of water in conventional simulations are high.
V. METHOLOGY
A. AMBER
Our aim is to work with the AMBER force field, defined
by the energy function.
Which consists of terms for bonds, angles, dihedrals, van
der Waals, and electrostatics. For most systems, these terms
are derived with the aid of the software Antechamber using
either an AMBER amino acid force field or the general AMBER
force field (GAFF). Antechamber assigns terms based on con-nectivity,
and generally the parameters work well for organic
systems. However, for metal complexes and for systems with
features not represented in the standard library set, many
terms are either unassigned or are inaccurate (and need to be
redone) QM Frequency Calculation for Bonds and Angles. To
obtain unassigned bond and angle terms, a sequence of
energy calculations needs to be done at both the QM and MM
levels. The difference between the potential energy surfaces
can then be fit to determine the harmonic constants. However,
this is generally a computationally expensive procedure. More
efficiently, these terms can be determined from a single
frequency calculation with the minimum energy state structure.
As with a relaxed scan, the vibrational frequencies can be
computed at both the QM level and the MM level, so that the
effects already present in the force field can be removed.
B. CHARMM
The force field parameters are developed at the restricted
Hartree-Fock (RHF) ab initio level of theory with the basis set
in consistency with the CHARMM parameterization of the
c35b2 release. All ab initio calculations are performed with the
Gaussian03 package revision, whereas classical force field
potential energies are computed with the NAMD package ,
which is also used for the evaluative MD simulations. The acid
dissociation constant (pKa) of rosiglitazone is estimated
with ALOGPS.
There are several versions of the CHARMM force
f ield available from the MacKerrell website. Don?t
let this confuse you! Most commonly you will see
CHARMM19,CHARMM22, or CHARMM27. CHARMM22
(released in 1991) and CHARMM27 (released in 1999) are the
most recent versions of the force field. For purely protein
systems, the two are equivalent. However, if you are
simulating any nucleic acids, be aware that CHARMM27 has
been optimized for simulating DNA and should be used.
VI. CONCLUSION
In this paper, we have presented a method for parametrizing
as AMBER force field that is largely independent of the choice
of coordinates. The method requires only a frequency
calculation and is able to determine unknown bond or angle
force constants from an existing partial parametrization. A
corresponding Python software package called parafreq was

3. 3
developed that allows researchers to easily determine
force constants for any system.
CHARMM based model has been derived for molecular
simulations, an important nuclear receptor ligand, relevant
pharmaceutical applications in the treatment of type II dia-betes.
The proposed force field allows MD studies of
rosigli-tazone and interactions with other compounds TZD
PPARC nuclear receptor and other proteins and other
biomolecular systems under CHARMM.
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