OBForceFieldGhemical

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OBForceFieldGhemical class

This class is an implementation of the molecular mechanics force field used in the Ghemical program. It is an all-atom method similar to the Tripos-5.2 force field.

Parameters

Parameters for the Gehmical force field can be found in data/ghemical.prm.

Bonded Interactions

Bond Stretching

BondEGhemical.png

E_{bond}=k_{b}(r_{ab}-r_{ab}^0)^2

k_b: bond stretching force constant (ghemical.prm)

r_{ab}^0: ideal bond length (ghemical.prm)

r_{ab}: bond length between atoms a and b

Angle Bending

AngleEGhemical.png

E_{angle}=k_a(\theta_{abc}-\theta_{abc}^0)^2

k_a: angle bending force constant (ghemical.prm)

\theta_{abc}^0: ideal angle (ghemical.prm)

\theta_{abc}: angle

Torsional

TorsionSingleEGhemical.png TorsionDoubleEGhemical.png

E_{torsion}= V_1(1 + cos(\omega_{abcd})) + V_2(1 - cos(2\omega_{abcd})) + V_1(1 + cos(3\omega_{abcd}))

V_t: rotational barrier (ghemical.prm)

s_t: +1 if staggered minimum, -1 if eclipsed minimum (ghemical.prm)

n_t: multiplicity (ghemical.prm)

\omega_{abcd}: torsion angle

V_1, V_2 and V_3 can be derived from V_t, s_t and n_t using this table:

s_tn_t=+3 s_tn_t=+2 s_tn_t=+1 s_tn_t=-1 s_tn_t=-2 s_tn_t=-3
V_1 0 0 V_t -V_t 0 0
V_2 0 -V_t 0 0 V_t 0
V_3 V_t 0 0 0 0 -V_t

Non-Bonded Interactions

Van der Waals

VDWEGhemical.png

E_{vdw}=k_{ab}\left(\frac{1}{\sigma_{ab}^{12}} - \frac{2}{\sigma_{ab}^6}\right)

k_{ab} = \sqrt{k_a k_b}: force constant (ghemical.prm)

\sigma_{ab} = \frac{r_{ab}}{R_a + R_b}

R_a: vdw radius of atom a (ghemical.prm)

r_{ab}: separation (calulated in the same way as bondlengths)

Electrostatic

EleAttrEGhemical.png EleRepEGhemical.png

E_{ele}=332.17 \frac{Q_a Q_b}{r_{ab}}

Q_a: net atomic charge on atom a

Q_b: net atomic charge on atom b

r_{ab}: separation (calulated in the same way as bondlengths)

332.17: unit conversion factor

1,4-Scaling

Non bonded interations between atoms in a 1,4 relationship are scaled with a factor 0.5.

Validation

In progress... (1,4-scaling problem)