Merge branch 'main' of github.com:Becksteinlab/SAMPL7_logP_data into …

…main

submissions/logP_prediction_Iorga_Beckstein_CGenFF.csv

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+# 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

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