diff --git a/submissions/logP_prediction_Iorga_Beckstein_CGenFF.csv b/submissions/logP_prediction_Iorga_Beckstein_CGenFF.csv new file mode 100644 index 0000000..a275215 --- /dev/null +++ b/submissions/logP_prediction_Iorga_Beckstein_CGenFF.csv @@ -0,0 +1,152 @@ +# OCTANOL TO WATER (ΔG_octanol - ΔG_water) TRANSFER FREE ENERGY PREDICTIONS +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# +# PREDICTION SECTION +# +# It is mandatory to submit water to octanol (ΔG_octanol - ΔG_water) transfer free energy (TFE) predictions for all 22 molecules. +# Incomplete submissions will not be accepted. +# The energy units must be in kcal/mol. +# +# Please report the general molecule `ID tag` in the form of `SMXX` (e.g. SM25, SM26, etc). +# Please indicate the microstate(s) used in the `Molecule ID/IDs considered (no commas)` section (e.g. `SM25_micro000`, SM25_extra001`) +# Please report TFE standard error of the mean (SEM) and TFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# ID tag, Molecule ID/IDs considered (no commas), TFE, TFE SEM, TFE model uncertainty, (optional) logD, (optional) SEM logD +# +# Your transfer free energy prediction for the neutral form does NOT have to be `SMXX_micro000` (which is the challenge provided neutral microstate). +# 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`. +# +# 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. +# +# 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. +# +# 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). +# If multiple microstates are used, please report the order of population in the aqueous phase in descending order. +# Please list microstate populations, SMILES strings and the molecule IDs in the `METHOD DESCRIPTION SECTION` section further below. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SM25,SM25_micro004,-6.55,0.18,1.50 +SM26,SM26_micro000,-2.39,0.11,1.50 +SM27,SM27_micro000,-3.31,0.13,1.50 +SM28,SM28_micro000,-2.52,0.13,1.50 +SM29,SM29_micro000,-2.64,0.15,1.50 +SM30,SM30_micro000,-5.73,0.14,1.50 +SM31,SM31_micro000,-4.16,0.13,1.50 +SM32,SM32_micro000,-5.95,0.16,1.50 +SM33,SM33_micro000,-7.44,0.16,1.50 +SM34,SM34_micro000,-6.08,0.14,1.50 +SM35,SM35_micro000,-2.70,0.36,1.50 +SM36,SM36_micro000,-3.65,0.60,1.50 +SM37,SM37_micro000,-3.31,0.75,1.50 +SM38,SM38_micro000,-2.26,0.41,1.50 +SM39,SM39_micro000,-5.10,0.41,1.50 +SM40,SM40_micro000,-3.54,0.31,1.50 +SM41,SM41_micro000,-3.53,0.18,1.50 +SM42,SM42_micro003,-7.01,0.13,1.50 +SM43,SM43_micro004,-5.10,0.16,1.50 +SM44,SM44_micro000,-1.15,0.22,1.50 +SM45,SM45_micro000,-5.15,0.41,1.50 +SM46,SM46_micro000,-3.13,0.29,1.50 +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Bogdan I. Iorga/Oliver Beckstein +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +ICSN, CNRS, Gif-sur-Yvette, France/Arizona State University, USA +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name must not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +# SAMPL7_logP_MDPOW_CGenFF +MD (CGenFF/TIP3P) +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +20,000 hours, CPU +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +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. +# +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gromacs 2020.3 +MDPOW 0.7.0-dev +CGENFF 2.2.0 +# +# METHOD CATEGORY SECTION +# +# State which method category your prediction method is better described as: +# `Physical (MM)`, `Physical (QM)`, `Empirical`, or `Mixed`. +# Pick only one category label. +# The `Category:` keyword is required. +Category: +Physical (MM) +# +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# +# If you have evaluated additional microstates, please report their SMILES strings and populations of all the microstates in this section. +# 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. +# +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +Alchemical free energy calculations were performed in explicit +solvent, following the protocol described in [1,2]. Parameters were generated with the +PARAMCHEM CGENFF program via the server at +https://cgenff.umaryland.edu/ for CHARMM/CGenFF with the CHARMM TIP3P +water model. Files were prepared for Gromacs 2020.3. The alchemical data were +analyzed with thermodynamic integration. Errors are reported as errors +of the mean (see [1,2]). The +model uncertainty was estimated on the basis of the results from [2]. +[1] Kenney, I. M., Beckstein, O., and Iorga, B. I. (2016) Prediction of cyclohexane-water +distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with +the OPLS-AA force field, J. Comput. Aided Mol. Des. 30(11):1045-1058 DOI: 10.1007/s10822-016-9949-5. +[2] Fan, S., Iorga, B. I., and Beckstein, O. (2020) Prediction of octanol-water partition coefficients for +the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields, +J Comput Aided Mol Des 34(5):543-560 DOI: 10.1007/s10822-019-00267-z. +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +True diff --git a/submissions/logP_prediction_Iorga_Beckstein_GAFF.csv b/submissions/logP_prediction_Iorga_Beckstein_GAFF.csv new file mode 100644 index 0000000..1bbd337 --- /dev/null +++ b/submissions/logP_prediction_Iorga_Beckstein_GAFF.csv @@ -0,0 +1,157 @@ +# OCTANOL TO WATER (ΔG_octanol - ΔG_water) TRANSFER FREE ENERGY PREDICTIONS +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# +# PREDICTION SECTION +# +# It is mandatory to submit water to octanol (ΔG_octanol - ΔG_water) transfer free energy (TFE) predictions for all 22 molecules. +# Incomplete submissions will not be accepted. +# The energy units must be in kcal/mol. +# +# Please report the general molecule `ID tag` in the form of `SMXX` (e.g. SM25, SM26, etc). +# Please indicate the microstate(s) used in the `Molecule ID/IDs considered (no commas)` section (e.g. `SM25_micro000`, SM25_extra001`) +# Please report TFE standard error of the mean (SEM) and TFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# ID tag, Molecule ID/IDs considered (no commas), TFE, TFE SEM, TFE model uncertainty, (optional) logD, (optional) SEM logD +# +# Your transfer free energy prediction for the neutral form does NOT have to be `SMXX_micro000` (which is the challenge provided neutral microstate). +# 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`. +# +# 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. +# +# 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. +# +# 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). +# If multiple microstates are used, please report the order of population in the aqueous phase in descending order. +# Please list microstate populations, SMILES strings and the molecule IDs in the `METHOD DESCRIPTION SECTION` section further below. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SM25,SM25_micro004,-4.76,0.33,1.50 +SM26,SM26_micro000,-1.60,0.20,1.50 +SM27,SM27_micro000,-3.84,0.35,1.50 +SM28,SM28_micro000,-3.08,0.34,1.50 +SM29,SM29_micro000,-3.18,0.24,1.50 +SM30,SM30_micro000,-5.30,0.42,1.50 +SM31,SM31_micro000,-4.34,0.25,1.50 +SM32,SM32_micro000,-4.57,0.24,1.50 +SM33,SM33_micro000,-5.64,0.24,1.50 +SM34,SM34_micro000,-5.10,0.32,1.50 +SM35,SM35_micro000,-2.44,0.49,1.50 +SM36,SM36_micro000,-4.92,0.47,1.50 +SM37,SM37_micro000,-3.78,0.42,1.50 +SM38,SM38_micro000,-2.59,0.53,1.50 +SM39,SM39_micro000,-5.06,0.54,1.50 +SM40,SM40_micro000,-4.77,0.49,1.50 +SM41,SM41_micro000,-3.37,0.38,1.50 +SM42,SM42_micro003,-5.75,0.28,1.50 +SM43,SM43_micro004,-3.91,0.24,1.50 +SM44,SM44_micro000,-3.11,0.25,1.50 +SM45,SM45_micro000,-4.91,0.28,1.50 +SM46,SM46_micro000,-4.10,0.19,1.50 +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Bogdan I. Iorga/Oliver Beckstein +# +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +ICSN, CNRS, Gif-sur-Yvette, France/Arizona State University, USA +# +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name must not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +# SAMPL7_logP_MDPOW_GAFF +MD (GAFF/TIP3P) +# +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +20,000 hours, CPU +# +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +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. +# +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gromacs 2020.3 +MDPOW 0.7.0-dev +AmberTools +ACPYPE 0 (2017) +# +# METHOD CATEGORY SECTION +# +# State which method category your prediction method is better described as: +# `Physical (MM)`, `Physical (QM)`, `Empirical`, or `Mixed`. +# Pick only one category label. +# The `Category:` keyword is required. +Category: +Physical (MM) +# +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# +# If you have evaluated additional microstates, please report their SMILES strings and populations of all the microstates in this section. +# 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. +# +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +Alchemical free energy calculations were performed in explicit +solvent, following the protocol described in [1,2]. Parameters were generated with +Antechamber from AmberTools and ACPYPE for AMBER (GAFF) with the TIP3P +water model. Files were prepared for Gromacs 2020.3. The alchemical data +were analyzed with thermodynamic integration. Errors are reported as +errors of the mean (see [1,2]). The +model uncertainty was estimated on the basis of the results from [2]. +[1] Kenney, I. M., Beckstein, O., and Iorga, B. I. (2016) Prediction of cyclohexane-water +distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with +the OPLS-AA force field, J. Comput. Aided Mol. Des. 30(11):1045-1058 DOI: 10.1007/s10822-016-9949-5. +[2] Fan, S., Iorga, B. I., and Beckstein, O. (2020) Prediction of octanol-water partition coefficients for +the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields, +J Comput Aided Mol Des 34(5):543-560 DOI: 10.1007/s10822-019-00267-z. +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False diff --git a/submissions/logP_prediction_Iorga_Beckstein_LigParGen.csv b/submissions/logP_prediction_Iorga_Beckstein_LigParGen.csv new file mode 100644 index 0000000..5fe13e9 --- /dev/null +++ b/submissions/logP_prediction_Iorga_Beckstein_LigParGen.csv @@ -0,0 +1,156 @@ +# OCTANOL TO WATER (ΔG_octanol - ΔG_water) TRANSFER FREE ENERGY PREDICTIONS +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# +# PREDICTION SECTION +# +# It is mandatory to submit water to octanol (ΔG_octanol - ΔG_water) transfer free energy (TFE) predictions for all 22 molecules. +# Incomplete submissions will not be accepted. +# The energy units must be in kcal/mol. +# +# Please report the general molecule `ID tag` in the form of `SMXX` (e.g. SM25, SM26, etc). +# Please indicate the microstate(s) used in the `Molecule ID/IDs considered (no commas)` section (e.g. `SM25_micro000`, SM25_extra001`) +# Please report TFE standard error of the mean (SEM) and TFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# ID tag, Molecule ID/IDs considered (no commas), TFE, TFE SEM, TFE model uncertainty, (optional) logD, (optional) SEM logD +# +# Your transfer free energy prediction for the neutral form does NOT have to be `SMXX_micro000` (which is the challenge provided neutral microstate). +# 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`. +# +# 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. +# +# 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. +# +# 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). +# If multiple microstates are used, please report the order of population in the aqueous phase in descending order. +# Please list microstate populations, SMILES strings and the molecule IDs in the `METHOD DESCRIPTION SECTION` section further below. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SM25,SM25_micro004,-2.06,0.74,1.50 +SM26,SM26_micro000,-1.32,0.33,1.50 +SM27,SM27_micro000,2.08,0.36,1.50 +SM28,SM28_micro000,-1.75,0.50,1.50 +SM29,SM29_micro000,2.47,0.50,1.50 +SM30,SM30_micro000,0.78,0.51,1.50 +SM31,SM31_micro000,-5.45,0.23,1.50 +SM32,SM32_micro000,-0.62,0.38,1.50 +SM33,SM33_micro000,-2.01,0.56,1.50 +SM34,SM34_micro000,-7.91,0.24,1.50 +SM35,SM35_micro000,4.17,0.46,1.50 +SM36,SM36_micro000,1.80,0.96,1.50 +SM37,SM37_micro000,-5.76,0.33,1.50 +SM38,SM38_micro000,1.61,0.54,1.50 +SM39,SM39_micro000,-3.43,0.50,1.50 +SM40,SM40_micro000,-3.47,0.56,1.50 +SM41,SM41_micro000,-2.79,0.26,1.50 +SM42,SM42_micro003,-4.40,0.41,1.50 +SM43,SM43_micro004,-6.70,0.35,1.50 +SM44,SM44_micro000,-2.46,0.27,1.50 +SM45,SM45_micro000,-4.59,0.46,1.50 +SM46,SM46_micro000,1.16,0.50,1.50 +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Bogdan I. Iorga/Oliver Beckstein +# +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +ICSN, CNRS, Gif-sur-Yvette, France/Arizona State University, USA +# +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name must not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +# SAMPL7_logP_MDPOW_LigParGen +MD LigParGen (OPLS-AA/TIP4P) +# +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +20,000 hours, CPU +# +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +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. +# +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gromacs 2020.3 +MDPOW 0.7.0-dev +LigParGen 2.1 +# +# METHOD CATEGORY SECTION +# +# State which method category your prediction method is better described as: +# `Physical (MM)`, `Physical (QM)`, `Empirical`, or `Mixed`. +# Pick only one category label. +# The `Category:` keyword is required. +Category: +Physical (MM) +# +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# +# If you have evaluated additional microstates, please report their SMILES strings and populations of all the microstates in this section. +# 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. +# +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +Alchemical free energy calculations were performed in explicit +solvent, following the protocol described in [1,2]. Parameters were generated with the +OPLS/CM1A LigParGen server http://zarbi.chem.yale.edu/ligpargen/ for +OPLS-AA with the TIP4P water model. Files were prepared for Gromacs +2020.3. The alchemical data were analyzed with thermodynamic +integration. Errors are reported as errors of the mean (see [1,2]). The +model uncertainty was estimated on the basis of the results from [2]. +[1] Kenney, I. M., Beckstein, O., and Iorga, B. I. (2016) Prediction of cyclohexane-water +distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with +the OPLS-AA force field, J. Comput. Aided Mol. Des. 30(11):1045-1058 DOI: 10.1007/s10822-016-9949-5. +[2] Fan, S., Iorga, B. I., and Beckstein, O. (2020) Prediction of octanol-water partition coefficients for +the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields, +J Comput Aided Mol Des 34(5):543-560 DOI: 10.1007/s10822-019-00267-z. +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False diff --git a/submissions/logP_prediction_Iorga_Beckstein_OPLS-AA.csv b/submissions/logP_prediction_Iorga_Beckstein_OPLS-AA.csv new file mode 100644 index 0000000..df7bf5b --- /dev/null +++ b/submissions/logP_prediction_Iorga_Beckstein_OPLS-AA.csv @@ -0,0 +1,152 @@ +# OCTANOL TO WATER (ΔG_octanol - ΔG_water) TRANSFER FREE ENERGY PREDICTIONS +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# +# PREDICTION SECTION +# +# It is mandatory to submit water to octanol (ΔG_octanol - ΔG_water) transfer free energy (TFE) predictions for all 22 molecules. +# Incomplete submissions will not be accepted. +# The energy units must be in kcal/mol. + +# Please report the general molecule `ID tag` in the form of `SMXX` (e.g. SM25, SM26, etc). +# Please indicate the microstate(s) used in the `Molecule ID/IDs considered (no commas)` section (e.g. `SM25_micro000`, SM25_extra001`) +# Please report TFE standard error of the mean (SEM) and TFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# ID tag, Molecule ID/IDs considered (no commas), TFE, TFE SEM, TFE model uncertainty, (optional) logD, (optional) SEM logD +# +# Your transfer free energy prediction for the neutral form does NOT have to be `SMXX_micro000` (which is the challenge provided neutral microstate). +# 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`. +# +# 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. +# +# 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. +# +# 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). +# If multiple microstates are used, please report the order of population in the aqueous phase in descending order. +# Please list microstate populations, SMILES strings and the molecule IDs in the `METHOD DESCRIPTION SECTION` section further below. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SM25,SM25_micro004,-4.97,0.30,1.50 +SM26,SM26_micro000,-1.88,0.31,1.50 +SM27,SM27_micro000,-2.69,0.25,1.50 +SM28,SM28_micro000,-1.92,0.36,1.50 +SM29,SM29_micro000,-0.91,0.25,1.50 +SM30,SM30_micro000,-5.97,0.24,1.50 +SM31,SM31_micro000,-5.45,0.23,1.50 +SM32,SM32_micro000,-5.13,0.30,1.50 +SM33,SM33_micro000,-6.61,0.31,1.50 +SM34,SM34_micro000,-7.91,0.24,1.50 +SM35,SM35_micro000,-1.07,0.45,1.50 +SM36,SM36_micro000,-5.22,0.51,1.50 +SM37,SM37_micro000,-5.76,0.33,1.50 +SM38,SM38_micro000,3.79,0.54,1.50 +SM39,SM39_micro000,-2.17,0.45,1.50 +SM40,SM40_micro000,-3.47,0.56,1.50 +SM41,SM41_micro000,-2.93,0.22,1.50 +SM42,SM42_micro003,-6.48,0.38,1.50 +SM43,SM43_micro004,-6.70,0.35,1.50 +SM44,SM44_micro000,-3.61,0.21,1.50 +SM45,SM45_micro000,-7.61,0.19,1.50 +SM46,SM46_micro000,-6.94,0.24,1.50 +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Bogdan I. Iorga/Oliver Beckstein +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +ICSN, CNRS, Gif-sur-Yvette, France/Arizona State University, USA +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name must not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +# SAMPL7_logP_MDPOW_OPLS-AA +MD (OPLS-AA/TIP4P) +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +20,000 hours, CPU +# +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +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. +# +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gromacs 2020.3 +MDPOW 0.7.0-dev +mol2ff +# METHOD CATEGORY SECTION +# +# State which method category your prediction method is better described as: +# `Physical (MM)`, `Physical (QM)`, `Empirical`, or `Mixed`. +# Pick only one category label. +# The `Category:` keyword is required. +Category: +Physical (MM) +# +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# +# If you have evaluated additional microstates, please report their SMILES strings and populations of all the microstates in this section. +# 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. +# +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +Alchemical free energy calculations were performed in explicit +solvent, following the protocol described in [1,2]. Parameters were generated with the +OPLSAA mol2ff software (B.I. Iorga, unpublished; also used in [1,2]) for +OPLS-AA with the TIP4P water model. Files were prepared for Gromacs +2020.3. The alchemical data were analyzed with thermodynamic +integration. Errors are reported as errors of the mean (see [1,2]). The +model uncertainty was estimated on the basis of the results from [2]. +[1] Kenney, I. M., Beckstein, O., and Iorga, B. I. (2016) Prediction of cyclohexane-water +distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with +the OPLS-AA force field, J. Comput. Aided Mol. Des. 30(11):1045-1058 DOI: 10.1007/s10822-016-9949-5. +[2] Fan, S., Iorga, B. I., and Beckstein, O. (2020) Prediction of octanol-water partition coefficients for +the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields, +J Comput Aided Mol Des 34(5):543-560 DOI: 10.1007/s10822-019-00267-z. +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False