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############################## | ||
## ## | ||
## Force Field Definition ## | ||
## ## | ||
############################## | ||
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forcefield OPLS-AA | ||
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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 | ||
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############################# | ||
## ## | ||
## Atom Type Definitions ## | ||
## ## | ||
############################# | ||
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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 | ||
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################################ | ||
## ## | ||
## Van der Waals Parameters ## | ||
## ## | ||
################################ | ||
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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 | ||
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################################## | ||
## ## | ||
## Bond Stretching Parameters ## | ||
## ## | ||
################################## | ||
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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 | ||
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################################ | ||
## ## | ||
## Angle Bending Parameters ## | ||
## ## | ||
################################ | ||
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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 | ||
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################################ | ||
## ## | ||
## Urey-Bradley Parameters ## | ||
## ## | ||
################################ | ||
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ureybrad 35 34 35 38.25 1.5537 | ||
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##################################### | ||
## ## | ||
## Improper Torsional Parameters ## | ||
## ## | ||
##################################### | ||
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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 | ||
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############################ | ||
## ## | ||
## Torsional Parameters ## | ||
## ## | ||
############################ | ||
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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 | ||
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torsion 0 0 0 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 | ||
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######################################## | ||
## ## | ||
## Atomic Partial Charge Parameters ## | ||
## ## | ||
######################################## | ||
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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 | ||
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.. _LigParGen: | ||
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******************** | ||
The LigParGen Server | ||
******************** | ||
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The `LigParGen Server` is a website maintained by the Jorgensen group at Yale University | ||
for generating OPLS-AA parameters for small molecules, with up to 200 atoms. These | ||
parameters are compatible with the published OPLS-AA forcefield and are useful for | ||
molecules that are not covered by OPLS-AA out of the box. | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
:titlesonly: | ||
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overview | ||
utility | ||
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.. _LigParGen Server: https://zarbi.chem.yale.edu/ligpargen/index.html |
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******** | ||
Overview | ||
******** | ||
The heart of the main webpage is this section: | ||
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.. figure:: images/ligpargen.png | ||
:align: center | ||
:alt: The LigParGen webpage | ||
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The LigParGen Webpage | ||
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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: | ||
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.. include:: images/ethane.key | ||
:literal: |
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********************** | ||
LigParGen utility tool | ||
********************** |