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| 1 | +# OCTANOL TO WATER (ΔG_octanol - ΔG_water) TRANSFER FREE ENERGY PREDICTIONS |
| 2 | +# |
| 3 | +# This file will be automatically parsed. It must contain the following four elements: |
| 4 | +# predictions, name of method, software listing, and method description. |
| 5 | +# These elements must be provided in the order shown with their respective headers. |
| 6 | +# |
| 7 | +# Any line that begins with a # is considered a comment and will be ignored when parsing. |
| 8 | +# |
| 9 | +# |
| 10 | +# PREDICTION SECTION |
| 11 | +# |
| 12 | +# It is mandatory to submit water to octanol (ΔG_octanol - ΔG_water) transfer free energy (TFE) predictions for all 22 molecules. |
| 13 | +# Incomplete submissions will not be accepted. |
| 14 | +# The energy units must be in kcal/mol. |
| 15 | +# |
| 16 | +# Please report the general molecule `ID tag` in the form of `SMXX` (e.g. SM25, SM26, etc). |
| 17 | +# Please indicate the microstate(s) used in the `Molecule ID/IDs considered (no commas)` section (e.g. `SM25_micro000`, SM25_extra001`) |
| 18 | +# Please report TFE standard error of the mean (SEM) and TFE model uncertainty. |
| 19 | +# |
| 20 | +# The data in each prediction line should be structured as follows: |
| 21 | +# ID tag, Molecule ID/IDs considered (no commas), TFE, TFE SEM, TFE model uncertainty, (optional) logD, (optional) SEM logD |
| 22 | +# |
| 23 | +# Your transfer free energy prediction for the neutral form does NOT have to be `SMXX_micro000` (which is the challenge provided neutral microstate). |
| 24 | +# If you use a microstate other than the challenge provided microstate, please fill out the `Molecule ID/IDs considered (no commas)` section using a molecule ID in the form of `SMXX_extra001` (number can vary) and please list the molecule ID and it's SMILES string in your methods description in the `METHOD DESCRIPTION SECTION`. |
| 25 | +# |
| 26 | +# You may optionally provide predicted logD values; these will be used as a consistency check on our estimated logD values if you submit both logP and pKa values. |
| 27 | +# |
| 28 | +# Only one entry in the second column (`Molecule ID/IDs considered (no commas)`) is required, but you should list all IDs considered/input to your calculations. See challenge instructions. |
| 29 | +# |
| 30 | +# If you have evaluated additional microstates then the molecule ID used in the `Molecule ID/IDs considered (no commas)` section needs to be in the format: `SMXX_extra001` (number can vary). |
| 31 | +# If multiple microstates are used, please report the order of population in the aqueous phase in descending order. |
| 32 | +# Please list microstate populations, SMILES strings and the molecule IDs in the `METHOD DESCRIPTION SECTION` section further below. |
| 33 | +# |
| 34 | +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. |
| 35 | +Predictions: |
| 36 | +SM25,SM25_micro004,-6.55,0.18,1.50 |
| 37 | +SM26,SM26_micro000,-2.39,0.11,1.50 |
| 38 | +SM27,SM27_micro000,-3.31,0.13,1.50 |
| 39 | +SM28,SM28_micro000,-2.52,0.13,1.50 |
| 40 | +SM29,SM29_micro000,-2.64,0.15,1.50 |
| 41 | +SM30,SM30_micro000,-5.73,0.14,1.50 |
| 42 | +SM31,SM31_micro000,-4.16,0.13,1.50 |
| 43 | +SM32,SM32_micro000,-5.95,0.16,1.50 |
| 44 | +SM33,SM33_micro000,-7.44,0.16,1.50 |
| 45 | +SM34,SM34_micro000,-6.08,0.14,1.50 |
| 46 | +SM35,SM35_micro000,-2.70,0.36,1.50 |
| 47 | +SM36,SM36_micro000,-3.65,0.60,1.50 |
| 48 | +SM37,SM37_micro000,-3.31,0.75,1.50 |
| 49 | +SM38,SM38_micro000,-2.26,0.41,1.50 |
| 50 | +SM39,SM39_micro000,-5.10,0.41,1.50 |
| 51 | +SM40,SM40_micro000,-3.54,0.31,1.50 |
| 52 | +SM41,SM41_micro000,-3.53,0.18,1.50 |
| 53 | +SM42,SM42_micro003,-7.01,0.13,1.50 |
| 54 | +SM43,SM43_micro004,-5.10,0.16,1.50 |
| 55 | +SM44,SM44_micro000,-1.15,0.22,1.50 |
| 56 | +SM45,SM45_micro000,-5.15,0.41,1.50 |
| 57 | +SM46,SM46_micro000,-3.13,0.29,1.50 |
| 58 | +# |
| 59 | +# |
| 60 | +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. |
| 61 | +Participant name: |
| 62 | +Bogdan I. Iorga/Oliver Beckstein |
| 63 | +# |
| 64 | +# |
| 65 | +# Please list your organization/affiliation, using only UTF-8 characters as described above. |
| 66 | +Participant organization: |
| 67 | +ICSN, CNRS, Gif-sur-Yvette, France/Arizona State University, USA |
| 68 | +# |
| 69 | +# |
| 70 | +# NAME SECTION |
| 71 | +# |
| 72 | +# Please provide an informal but informative name of the method used. |
| 73 | +# The name must not exceed 40 characters. |
| 74 | +# The 'Name:' keyword is required as shown here. |
| 75 | +Name: |
| 76 | +# SAMPL7_logP_MDPOW_CGenFF |
| 77 | +MD (CGenFF/TIP3P) |
| 78 | +# |
| 79 | +# |
| 80 | +# COMPUTE TIME SECTION |
| 81 | +# |
| 82 | +# Please provide the average compute time across all of the molecules. |
| 83 | +# For physical methods, report the GPU and/or CPU compute time in hours. |
| 84 | +# For empirical methods, report the query time in hours. |
| 85 | +# Create a new line for each processor type. |
| 86 | +# The 'Compute time:' keyword is required as shown here. |
| 87 | +Compute time: |
| 88 | +20,000 hours, CPU |
| 89 | +# |
| 90 | +# COMPUTING AND HARDWARE SECTION |
| 91 | +# |
| 92 | +# Please provide details of the computing resources that were used to train models and make predictions. |
| 93 | +# Please specify compute time for training models and querying separately for empirical prediction methods. |
| 94 | +# Provide a detailed description of the hardware used to run the simulations. |
| 95 | +# The 'Computing and hardware:' keyword is required as shown here. |
| 96 | +Computing and hardware: |
| 97 | +All the simulations were performed in parallel (8 cores for each simulation) on cluster nodes running with CentOS6 and 4 CPU Intel Xeon E5-4627 v3 @ 2.60GHz. |
| 98 | +# |
| 99 | +# SOFTWARE SECTION |
| 100 | +# |
| 101 | +# List all major software packages used and their versions. |
| 102 | +# Create a new line for each software. |
| 103 | +# The 'Software:' keyword is required. |
| 104 | +Software: |
| 105 | +Gromacs 2020.3 |
| 106 | +MDPOW 0.7.0-dev |
| 107 | +CGENFF 2.2.0 |
| 108 | +# |
| 109 | +# METHOD CATEGORY SECTION |
| 110 | +# |
| 111 | +# State which method category your prediction method is better described as: |
| 112 | +# `Physical (MM)`, `Physical (QM)`, `Empirical`, or `Mixed`. |
| 113 | +# Pick only one category label. |
| 114 | +# The `Category:` keyword is required. |
| 115 | +Category: |
| 116 | +Physical (MM) |
| 117 | +# |
| 118 | +# METHOD DESCRIPTION SECTION |
| 119 | +# |
| 120 | +# Methodology and computational details. |
| 121 | +# Level of details should be roughly equivalent to that used in a publication. |
| 122 | +# Please include the values of key parameters with units. |
| 123 | +# Please explain how statistical uncertainties were estimated. |
| 124 | +# |
| 125 | +# If you have evaluated additional microstates, please report their SMILES strings and populations of all the microstates in this section. |
| 126 | +# If you used a microstate other than the challenge provided microstate (`SMXX_micro000`), please list your chosen `Molecule ID` (in the form of `SMXX_extra001`) along with the SMILES string in your methods description. |
| 127 | +# |
| 128 | +# Use as many lines of text as you need. |
| 129 | +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. |
| 130 | +Method: |
| 131 | +Alchemical free energy calculations were performed in explicit |
| 132 | +solvent, following the protocol described in [1,2]. Parameters were generated with the |
| 133 | +PARAMCHEM CGENFF program via the server at |
| 134 | +https://cgenff.umaryland.edu/ for CHARMM/CGenFF with the CHARMM TIP3P |
| 135 | +water model. Files were prepared for Gromacs 2020.3. The alchemical data were |
| 136 | +analyzed with thermodynamic integration. Errors are reported as errors |
| 137 | +of the mean (see [1,2]). The |
| 138 | +model uncertainty was estimated on the basis of the results from [2]. |
| 139 | +[1] Kenney, I. M., Beckstein, O., and Iorga, B. I. (2016) Prediction of cyclohexane-water |
| 140 | +distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with |
| 141 | +the OPLS-AA force field, J. Comput. Aided Mol. Des. 30(11):1045-1058 DOI: 10.1007/s10822-016-9949-5. |
| 142 | +[2] Fan, S., Iorga, B. I., and Beckstein, O. (2020) Prediction of octanol-water partition coefficients for |
| 143 | +the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields, |
| 144 | +J Comput Aided Mol Des 34(5):543-560 DOI: 10.1007/s10822-019-00267-z. |
| 145 | +# |
| 146 | +# All submissions must either be ranked or non-ranked. |
| 147 | +# Only one ranked submission per participant is allowed. |
| 148 | +# Multiple ranked submissions from the same participant will not be judged. |
| 149 | +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. |
| 150 | +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) |
| 151 | +Ranked: |
| 152 | +True |
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