Overview#
The heart of the main webpage is this section:
The LigParGen Webpage#
At the top you enter your structure as either SMILES or a Mol or PDB file. After choosing the charge model and specifying the charge, if any, click on Submit Molecule. For example, if you enter CC for ethane as the SMILES, select the 1.14* CMA1-LBCC charge model and submit it, you will be sent to a page where you can download the parameters in formats suitable for various simulation codes. The KEY file for Tinker is easy to read if bit verbose:
##############################
## ##
## Force Field Definition ##
## ##
##############################
forcefield OPLS-AA
vdwindex TYPE
vdwtype LENNARD-JONES
radiusrule GEOMETRIC
radiustype SIGMA
radiussize DIAMETER
epsilonrule GEOMETRIC
torsionunit 1.0
imptorunit 1.0
vdw-14-scale 2.0
chg-14-scale 2.0
electric 332.06
dielectric 1.0
#############################
## ##
## Atom Type Definitions ##
## ##
#############################
atom 800 800 CT "C00" 6 12.011 4
atom 801 801 CT "C01" 6 12.011 4
atom 802 802 HC "H02" 1 1.008 1
atom 803 803 HC "H03" 1 1.008 1
atom 804 804 HC "H04" 1 1.008 1
atom 805 805 HC "H05" 1 1.008 1
atom 806 806 HC "H06" 1 1.008 1
atom 807 807 HC "H07" 1 1.008 1
################################
## ##
## Van der Waals Parameters ##
## ##
################################
vdw 800 3.5000 0.0660
vdw 801 3.5000 0.0660
vdw 802 2.5000 0.0300
vdw 803 2.5000 0.0300
vdw 804 2.5000 0.0300
vdw 805 2.5000 0.0300
vdw 806 2.5000 0.0300
vdw 807 2.5000 0.0300
##################################
## ##
## Bond Stretching Parameters ##
## ##
##################################
bond 801 800 268.00 1.5290
bond 802 800 340.00 1.0900
bond 803 800 340.00 1.0900
bond 804 800 340.00 1.0900
bond 805 801 340.00 1.0900
bond 806 801 340.00 1.0900
bond 807 801 340.00 1.0900
################################
## ##
## Angle Bending Parameters ##
## ##
################################
angle 801 800 802 37.50 110.70
angle 801 800 803 37.50 110.70
angle 801 800 804 37.50 110.70
angle 800 801 805 37.50 110.70
angle 800 801 806 37.50 110.70
angle 800 801 807 37.50 110.70
angle 802 800 803 33.00 107.80
angle 802 800 804 33.00 107.80
angle 805 801 806 33.00 107.80
angle 805 801 807 33.00 107.80
angle 806 801 807 33.00 107.80
angle 803 800 804 33.00 107.80
################################
## ##
## Urey-Bradley Parameters ##
## ##
################################
ureybrad 35 34 35 38.25 1.5537
#####################################
## ##
## Improper Torsional Parameters ##
## ##
#####################################
imptors 801 802 800 803 0.000 180.0 2
imptors 801 802 800 804 0.000 180.0 2
imptors 800 805 801 806 0.000 180.0 2
imptors 800 805 801 807 0.000 180.0 2
############################
## ##
## Torsional Parameters ##
## ##
############################
torsion 805 801 800 802 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 806 801 800 804 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 805 801 800 804 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 807 801 800 803 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 807 801 800 802 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 807 801 800 804 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 806 801 800 802 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 805 801 800 803 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 806 801 800 803 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3
torsion 0 0 0 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3
########################################
## ##
## Atomic Partial Charge Parameters ##
## ##
########################################
charge 800 -0.2396
charge 801 -0.2396
charge 802 0.0799
charge 803 0.0799
charge 804 0.0799
charge 805 0.0799
charge 806 0.0799
charge 807 0.0799