Skip to content

Commit

Permalink
Merge pull request #35 from molssi-seamm/dev
Browse files Browse the repository at this point in the history 
Added customizable local forcefields and LigParGen interface.
  • Loading branch information
@seamm
seamm authored Jun 29, 2024
2 parents cc4573f + d9aff93 commit d1598eb
Show file tree
Hide file tree
Showing 10 changed files with 1,184 additions and 74 deletions.
6 changes: 6 additions & 0 deletions HISTORY.rst
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,12 @@
=======
History
=======
2024.6.28 -- Added customizable local forcefields and LigParGen interface.
* Added the machinery to handle local forcefield files in either
~/.seamm.d/data/Forcefields (personal) or ~/SEAMM/data/Forcefields (site).
* Added 'ligpargen' command to access custom parameters from the LigParGen service
at Yale University, ading them to the 'ligpargen.frc' personal forcefield, which
is automatically included in 'oplsaa.frc' if it exists.

2024.1.10 -- Fixed PF6- issue in CL&P forcefield
* The angle parameters for PF6- in the CL&P forcefield only work if the 180º F-P-F
Expand Down
4 changes: 4 additions & 0 deletions devtools/conda-envs/test_env.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,11 @@ dependencies:

# SEAMM
- kim-query
- pyperclip
- rdkit
- seamm
- seamm-ff-util
- tabulate

# Testing
- black
Expand All @@ -26,5 +29,6 @@ dependencies:

# Pip-only installs
- pip:
- read-structure-step
# Documentation
- sphinx-copybutton
149 changes: 135 additions & 14 deletions forcefield_step/data/oplsaa.frc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,18 @@

! Version Ref Function Label
!--------- --- ------------------------------ ------
2023.01.29 1 atom_types oplsaa CL&P
2023.01.29 1 atom_types oplsaa CL&P ligpargen:optional
2023.01.29 1 equivalence oplsaa CL&P
2023.01.29 1 charges oplsaa CL&P
2023.01.29 1 nonbond(12-6) oplsaa CL&P
2023.01.29 1 quadratic_bond oplsaa CL&P
2023.01.29 1 quadratic_angle oplsaa CL&P
2023.08.21 1 quadratic_angle oplsaa CL&P
2023.01.29 1 charges oplsaa CL&P ligpargen:optional
2023.01.29 1 nonbond(12-6) oplsaa CL&P ligpargen:optional
2023.01.29 1 quadratic_bond oplsaa CL&P ligpargen:optional
2023.01.29 1 quadratic_angle oplsaa CL&P ligpargen:optional
2023.08.21 1 quadratic_angle oplsaa CL&P ligpargen:optional
2023.08.26 1 tabulated_angle CL&P
2023.01.29 1 torsion_opls oplsaa CL&P
2023.01.29 1 improper_opls oplsaa
2023.01.29 1 torsion_opls oplsaa CL&P ligpargen:optional
2023.01.29 1 improper_opls oplsaa ligpargen:optional
2023.01.29 1 templates oplsaa
2024.06.20 1 fragments ligpargen:optional
#end

#define oplsaa
Expand Down Expand Up @@ -49,7 +50,7 @@
2023.01.29 1 templates CL&P
#end


#include local:OPLS-AA/ligpargen.frc missing_ok

#atom_types oplsaa

Expand Down Expand Up @@ -11262,6 +11263,31 @@
@Author Paul Saxe
@Date 2023-01-29
OPLSAA forcefield translated from Tinker version.

@bibtex @ARTICLE{Jorgensen2005-uh,
title = "Potential energy functions for atomic-level simulations of water
and organic and biomolecular systems",
author = "Jorgensen, William L and Tirado-Rives, Julian",
abstract = "An overview is provided on the development and status of
potential energy functions that are used in atomic-level
statistical mechanics and molecular dynamics simulations of
water and of organic and biomolecular systems. Some topics that
are considered are the form of force fields, their
parameterization and performance, simulations of organic
liquids, computation of free energies of hydration, universal
extension for organic molecules, and choice of atomic charges.
The discussion of water models covers some history, performance
issues, and special topics such as nuclear quantum effects.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
publisher = "Proceedings of the National Academy of Sciences",
volume = 102,
number = 19,
pages = "6665--6670",
month = may,
year = 2005,
language = "en",
doi = "10.1073/pnas.0408037102"
}
#end

#reference 2
Expand All @@ -11273,8 +11299,7 @@ Modeling Ionic Liquids Using a Systematic All-Atom Force Field.
J Phys Chem B 2004, 108 (6), 2038–2047.
https://doi.org/10.1021/jp0362133.


@article{10.1021/jp0362133,
@bibtex @article{10.1021/jp0362133,
year = {2004},
title = {{Modeling Ionic Liquids Using a Systematic All-Atom Force Field}},
author = {Lopes, José N. Canongia and Deschamps, Johnny and Pádua, Agílio A. H.},
Expand All @@ -11296,8 +11321,7 @@ Molecular Force Field for Ionic Liquids Composed of Triflate or Bistriflylimide
J Phys Chem B 2004, 108 (43), 16893–16898.
https://doi.org/10.1021/jp0476545.


@article{10.1021/jp0476545,
@bibtex @article{10.1021/jp0476545,
year = {2004},
title = {{Molecular Force Field for Ionic Liquids Composed of Triflate or Bistriflylimide Anions}},
author = {Lopes, José N. Canongia and Pádua, Agílio A. H.},
Expand Down Expand Up @@ -11326,6 +11350,103 @@ added missing angle parameters

from LibParGen on EC and FEC (ethylene carbonate and fluoroethylene carbonate)

Potential energy functions for atomic-level simulations of water and organic and
biomolecular systems. Jorgensen, W. L.; Tirado-Rives, J. Proc. Nat. Acad. Sci.
USA 2005, 102, 6665-6670

Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations.
Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L.
J. Phys. Chem. B, 2017, 121 (15), 3864-3870

LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands.
Dodda, L. S.;Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L.
Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331-W336

@bibtex @ARTICLE{Jorgensen2005-uh,
title = "Potential energy functions for atomic-level simulations of water
and organic and biomolecular systems",
author = "Jorgensen, William L and Tirado-Rives, Julian",
abstract = "An overview is provided on the development and status of
potential energy functions that are used in atomic-level
statistical mechanics and molecular dynamics simulations of
water and of organic and biomolecular systems. Some topics that
are considered are the form of force fields, their
parameterization and performance, simulations of organic
liquids, computation of free energies of hydration, universal
extension for organic molecules, and choice of atomic charges.
The discussion of water models covers some history, performance
issues, and special topics such as nuclear quantum effects.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
publisher = "Proceedings of the National Academy of Sciences",
volume = 102,
number = 19,
pages = "6665--6670",
month = may,
year = 2005,
language = "en"
}

@bibtex @ARTICLE{Dodda2017-hm,
title = "{1.14*CM1A-LBCC}: Localized bond-charge corrected {CM1A} charges
for condensed-phase simulations",
author = "Dodda, Leela S and Vilseck, Jonah Z and Tirado-Rives, Julian and
Jorgensen, William L",
abstract = "The quality of the 1.14*CM1A and 1.20*CM5 charge models was
evaluated for calculations of free energies of hydration. For a
set of 426 neutral molecules, 1.14*CM1A and 1.20*CM5 yield MADs
of 1.26 and 1.21 kcal/mol, respectively. The 1.14*CM1A charges,
which can be readily obtained for large systems, exhibit large
deviations only for a subset of functional groups. The results
for these cases were systematically improved using localized
bond-charge corrections (LBCC) by which offsetting adjustments
are made to the partial charges for atoms in specified bond
types. Only 19 LBCCs were needed to yield 1.14*CM1A-LBCC charges
that reduce the errors for the 426 $\Delta$Ghyd values to only
0.61 kcal/mol. The modified charge method was also tested in
computation of heats of vaporization and densities for pure
organic liquids, yielding average errors of 1.40 kcal/mol and
0.024 g/cm3, similar to those for 1.14*CM1A.",
journal = "J. Phys. Chem. B",
publisher = "American Chemical Society (ACS)",
volume = 121,
number = 15,
pages = "3864--3870",
month = apr,
year = 2017,
language = "en",
doi = "10.1021/acs.jpcb.7b00272"
}

@bibtex @ARTICLE{Dodda2017-in,
title = "{LigParGen} web server: an automatic {OPLS-AA} parameter
generator for organic ligands",
author = "Dodda, Leela S and Cabeza de Vaca, Israel and Tirado-Rives,
Julian and Jorgensen, William L",
journal = "Nucleic Acids Res.",
publisher = "Oxford University Press (OUP)",
volume = 45,
number = "W1",
pages = "W331--W336",
month = jul,
year = 2017,
copyright = "http://creativecommons.org/licenses/by-nc/4.0/",
doi = "10.1093/nar/gkx312"
}


@bibtex @Misc{SBLRHMKNNHXPHG-UWTATZPHSA-N,
author = "Dodda, Leela S and Cabeza de Vaca, Israel and Tirado-Rives,
Julian and Jorgensen, William L",
title = "{LigParGen} generated parameters for O=C1OCCO1 and O=C1OCC(F)O1
(1,3-dioxolan-2-one and (4S)-4-fluoro-1,3-dioxolan-2-one)",
month = "jun",
year = "2024",
organization = "William L. Jorgensen research group, Yale University",
url = "https://traken.chem.yale.edu/ligpargen/",
address = "New Haven, CT, USA",
note = "Accessed on 2024-06-26T11:29:43.355106"
}

#reference 5
@Author Paul Saxe
@Date 2023-09-13
Expand All @@ -11334,7 +11455,7 @@ from asymmetrical substitutions to a consistent force field model.
Phys. Chem. Chem. Phys. 19, 29617–29624 (2017).
doi: 10.1039/c7cp06081e

@article{10.1039/c7cp06081e,
@bibtex @article{10.1039/c7cp06081e,
year = {2017},
title = {{Ionic liquids with anions based on fluorosulfonyl derivatives: from asymmetrical substitutions to a consistent force field model}},
author = {Gouveia, Andreia S. L. and Bernardes, Carlos E. S. and Tomé, Liliana C. and Lozinskaya, Elena I. and Vygodskii, Yakov S. and Shaplov, Alexander S. and Lopes, José N. Canongia and Marrucho, Isabel M.},
Expand Down
Loading

0 comments on commit d1598eb

Please sign in to comment.