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
load_bace_example()	Load Amber Bace example perturbation.
load_simplesolvated()	Load the Amber solvated dataset.
load_invalidfiles()	Load the invalid files.
load_testfiles()	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.

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 [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.

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 [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.

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

• 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:

Bunch

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

• no_spaces_around_equal.out.bz2: AMBER output file where there are no spaces around the ‘=’ sign in the ‘ begin time read from’ section

• no_starting_simulation_time.out.bz2: AMBER output file where the starting simulation time is not read

Added in version 0.7.0.

alchemtest.amber.load_testfiles()

Load incomplete or wrongly formatted files to be used to test the AMBER parsers.

Returns:

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

• ’data’ : the data files

• ’DESCR’: the full description of all the files

Return type:

Bunch