Data for SAMPL6 Part II paper

• data: The latest archived version of the data can be found on Zenodo by following the DOI on the badge. If you want to refer to the data over all versions use DOI 10.5281/zenodo.3549988.

  Data are released under CC0. Code is released under the MIT license.

• paper: (please cite when using these data)

  S. Fan, B. I. Iorga, and O. Beckstein. Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. Journal of Computer-Aided Molecular Design, 34:543–560, 2020. DOI: 10.1007/s10822-019-00267-z

Background

The SAMPL6 (Part II) logP Challenge consists of predicting the octanol-water partition coefficients (log P) of 11 small molecules that resemble fragments of small molecule protein kinase inhibitors. Our aim is to evaluate how well current models can capture the transfer free energy of small molecules between different solvent environments through blind predictions.

This repository contains all data discussed in our paper Prediction of octanol-water partition coefficients for the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields in the SAMPL6 Special Issue of the Journal of Computer-Aided Molecular Design.

Input files

Topology input files for Gromacs 2018 are provided in the 02_top directory and its subdirectories for the different compounds and force fields.

Simulations were set up and managed with mdpow (0.7.0 development version, equivalent to commit 20152ad9723fa5ad9d039362233da07b5fa7811a).

Note: CHARMM simulations were performed with the CHARMM TIP3P water model (LJ interactions on hydrogens) whereas AMBER simulations were performed with the standard TIP3P water model. We used the TIP3P input files provided by Gromacs. The paper was not clear on this distinction between the two TIP3P water models.

SAMPL6 submission

• Directory 03_prep_submission contains scripts to generate the submission files from Google Sheets (which we used for aggregating data). They are not strictly necessary as supporting information but might be of interest for anyone who wants to do something similar (although this was more of an experiment than a workflow we would generally recommend).

• Directory 04_submission contains the data for our SAMPL6 submissions as CSV files.

  number	ID	force field	octanol
  1	sqosi	AMBER/GAFF	dry
  2	6nmtt	AMBER/GAFF	wet
  3	eufcy	OPLSAA/LigParGen	dry
  4	mwuua	OPLSAA/LigParGen	wet
  5	cp8kv	OPLSAA/transferrable	dry
  6	623c0	OPLSAA/transferrable	wet
  7	3oqhx	CHARMM/CGENFF	dry

• Directory 06_data contains the same data but organized by force field and molecule.

Improved protocol

The paper discusses improvements to our protocol. The data for these calculations can be found in directory 07_alchemlyb_results.