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 Amber Bace improper solvated vdw example |
|
Load Amber Bace example perturbation. |
|
Load the Amber solvated dataset. |
|
Load the invalid files. |
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Load incomplete or wrongly formatted files to be used to test the AMBER parsers. |
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 [Wang2015b].
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.
- Wang2015b
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.
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 [Wang2015a].
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.
- Wang2015a
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.
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 [Wang2015c].
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.
- Wang2015c
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.
Amber TI invalid output files¶
Examples for file validation testing.
Notes¶
no_useful_data.out.tar.bz2: file contains no useful data
no_control_data.out.tar.bz2: file contains no control data
no_temp0_setted.out.tar.bz2: file with Non-constant temperature
no_free_energy_info.out.tar.bz2: file with no free energy section
no_atomic_section.out.tar.bz2: file with no ATOMIC section
no_results_section.out.tar.bz2: file with no RESULTS section
Deprecated since version 0.7: use load_testfiles()
instead
-
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
Deprecated since version 0.7: use
load_testfiles()
instead
Amber: invalid/incomplete output files¶
Here we collected some invalid/incomplete AMBER output files that can be used to test specific part of the amber parser.
Notes¶
no_atomic_section.out.bz2: AMBER output file without the ATOMIC section
no_control_data.out.bz2: AMBER output file without the ‘2. CONTROL DATA FOR ‘ section
no_dHdl_data_points.out.bz2: AMBER output file with TI active, but no DV/DL values,
no_free_energy_info.out.bz2: AMBER output file without the settings regarding the free energy calculation
no_results_section.out.bz2: AMBER output file without the RESULT section
no_temp0_set.out.bz2: AMBER output file with temp0 not set
no_useful_data.out.bz2: AMBER output file without useful data, truncated after the header
none_in_mbar.out.bz2: AMBER output file with a wrongly formatted MBAR section. Specifically, a lambda value in a MBAR section has been altered, so it dowsn’t match with the other MBAR sections and the expected lambda values (0.2500 –> 0.2550)
not_finished_run.out.bz2: AMBER output file from an unterminated run
high_number_of_mbar_windows.out.bz2: AMBER output file from a run with high number of MBAR lambdas
New in version 0.7.0.