Amber datasets¶

Amber molecular dynamics simulation datasets.

The alchemlyb.amber module features datasets generated using the Amber molecular dynamics engine. They can be accessed using the following accessor functions:

`load_bace_improper`()	Load Amber Bace improper solvated vdw example :returns: data – Dictionary-like object, the interesting attributes are:
`load_bace_example`()	Load Amber Bace example perturbation.
`load_simplesolvated`()	Load the Amber solvated dataset.
`load_invalidfiles`()	Load the invalid files.

Amber: Small molecule thermodynamic integration free energy difference in water¶

Improper Bace solvated small molecule perturbation, alchemical vdw perturbation of ligand 1 into ligand 2. This example uses ligands CAT-13a to CAT-13m from [Wang2015].

Notes¶

Data Set Characteristics:

Number of Legs: 1 (vdw)
Number of Windows: 12
Length of Windows: 1ns
System Size: 3920 atoms
Temperature: 300 K
Pressure: 1 bar
Alchemical Pathway: vdw in ligand 1 –> vdw in ligand 2, softcore is used in vdw
Experimental Free Energy difference: N/A
Missing Values: None
Energy unit: kcal/mol
Time unit: ps
Date: Jan 2018
Donor: Silicon Therapeutics
License: CC0 Public Domain Dedication

This dataset was generated using the Amber molecular dynamics engine.

Wang2015: L. Wang, Y. Wu, Y. Deng, B. Kim, L. Pierce, G. Krilov, D. Lupyan, S. Robinson, M. K. Dahlgren, J. Greenwood, D. L. Romero, C. Masse, J. L. Knight, T. Steinbrecher, T. Beuming, W. Damm, E. Harder, W. Sherman, M. Brewer, R. Wester, M. Murcko, L. Frye, R. Farid, T. Lin, D. L. Mobley, W. L. Jorgensen, B. J. Berne, R. A. Friesner, and R. Abel. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society, 137(7):2695–2703, 2015. PMID: 25625324. DOI: 10.1021/ja512751q.

alchemtest.amber.load_bace_improper()¶

Load Amber Bace improper solvated vdw example :returns: data – Dictionary-like object, the interesting attributes are:

‘data’ : the data files for improper solvated vdw alchemical leg

Return type: Bunch

Amber: Small molecule thermodynamic integration free energy difference in water¶

Bace complex and solvated small molecule perturbation, alchemical perturbation of ligand 1 into ligand 2. This example uses ligands CAT-13d to CAT-17a from [Wang2015].

Notes¶

Data Set Characteristics:

Number of Legs: 3 (decharge, vdw, recharge)
Number of Windows: 5 for decharge, 12 for vdw, 5 for recharge
Length of Windows: 1ns
System Size: 46594 atoms (complex), 4115 atoms (solvated)
Temperature: 300 K
Pressure: 1 bar
Alchemical Pathway: (decharge + vdw + recharge) in ligand 1 –> (decharge + vdw + recharge) in ligand 2, decharge, vdw, and recharge are running in parellel, soft core is used in vdw
Experimental Free Energy difference: -0.26 kcal/mol
Missing Values: None
Energy unit: kcal/mol
Time unit: ps
Date: Jan 2018
Donor: Silicon Therapeutics
License: CC0 Public Domain Dedication

This dataset was generated using the Amber molecular dynamics engine.

Wang2015: L. Wang, Y. Wu, Y. Deng, B. Kim, L. Pierce, G. Krilov, D. Lupyan, S. Robinson, M. K. Dahlgren, J. Greenwood, D. L. Romero, C. Masse, J. L. Knight, T. Steinbrecher, T. Beuming, W. Damm, E. Harder, W. Sherman, M. Brewer, R. Wester, M. Murcko, L. Frye, R. Farid, T. Lin, D. L. Mobley, W. L. Jorgensen, B. J. Berne, R. A. Friesner, and R. Abel. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society, 137(7):2695–2703, 2015. PMID: 25625324. DOI: 10.1021/ja512751q.

alchemtest.amber.load_bace_example()¶

Load Amber Bace example perturbation. :returns: data – Dictionary-like object, the interesting attributes are:

‘data’ : the data files by system and alchemical leg

Return type: Bunch

Amber: Small molecule thermodynamic integration free energy difference in water¶

Small molecule perturbation in water, alchemically turned ligand 1 into ligand 2 in water. This example uses ligands 17124-1 to 18637-1 from [Wang2015].

Notes¶

Data Set Characteristics:

Number of Legs: 2 (charge, vdw)
Number of Windows: 5 for charge, 12 for vdw
Length of Windows: 1ns
System Size: 5979 atoms
Temperature: 300 K
Pressure: 1 bar
Alchemical Pathway: (charge + vdw) in ligand 1 –> (charge + vdw) in ligand 2, charge and vdw are running in parellel, soft core is used in vdw
Experimental Free Energy difference: N/A
Missing Values: None
Energy unit: kcal/mol
Time unit: ps
Date: Oct 2017
Donor: Silicon Therapeutics
License: CC0 Public Domain Dedication

This dataset was generated using the Amber molecular dynamics engine.

Wang2015: L. Wang, Y. Wu, Y. Deng, B. Kim, L. Pierce, G. Krilov, D. Lupyan, S. Robinson, M. K. Dahlgren, J. Greenwood, D. L. Romero, C. Masse, J. L. Knight, T. Steinbrecher, T. Beuming, W. Damm, E. Harder, W. Sherman, M. Brewer, R. Wester, M. Murcko, L. Frye, R. Farid, T. Lin, D. L. Mobley, W. L. Jorgensen, B. J. Berne, R. A. Friesner, and R. Abel. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society, 137(7):2695–2703, 2015. PMID: 25625324. DOI: 10.1021/ja512751q.

alchemtest.amber.load_simplesolvated()¶

Load the Amber solvated dataset.

Returns

data – Dictionary-like object, the interesting attributes are:

’data’ : the data files by alchemical leg
’DESCR’: the full description of the dataset

Return type

Bunch

Amber TI invalid output files¶

Examples for file validation testing.

Notes¶

invalid-case-1.out.bz2: file contains no useful data
invalid-case-2.out.bz2: file contains no control data
invalid-case-3.out.bz2: file with Non-constant temperature
invalid-case-4.out.bz2: file with no free energy section
invalid-case-5.out.bz2: file with no ATOMIC section
invalid-case-6.out.bz2: file with no RESULTS section

alchemtest.amber.load_invalidfiles()¶

Load the invalid files.

Returns

data – Dictionary-like object, the interesting attributes are:

’data’ : the example of invalid data files
’DESCR’: the full description of the dataset

Return type

Bunch