GDCC_submissions.txt

# Results for SAMPL8 GDCC Sterics and Flexibility Challenge
#
# This file will be automatically parsed.  It must contain the following seven elements:
# predictions, participant name, participant organization, name of method, software listing, method, method category, and ranked.
# These elements must be provided in the order shown.
# The file name must begin with the word "GDCC" and then be followed by an underscore or dash.
#
# FILE FORMAT: All comment lines in this file (which begin with #) will be ignored.
# Please use only UTF-8 characters in the non-comment fields. If your information (e.g. your name, etc.)
# contains a non-UTF-8 character, you may note it in comments near that entry.
#
#
# PREDICTIONS
# Please explicitly describe how you handle ions and pKa effects.
#
# The data in each prediction line should be structured as follows, with all (up to six) numbers in kcal/mol.
# host-guest ID (note that the host varies!), Free energy, free energy SEM, free energy model uncertainty,
# enthalpy, enthalpy SEM, enthalpy model uncertainty
# The free energy, free energy SEM, and free energy model uncertainty are REQUIRED.
# The corresponding quantities for binding enthalpy are optional.
#
# Note that the "model uncertainty" should be your estimate of ACCURACY of this particular approach
# for the compound considered.
#
# For the GDCC challenge, TEMOA-G3 binding values will not be judged, as literature values are available.
# Note there are two sets of hosts TEMOA and TEETOA.
#
# The list of predictions must begin with the "Prediction:" keyword, as illustrated here.
Predictions:
TEMOA-G1, -10.1, 0.1, 1.0, -0.3, 0.1, 1.0
TEMOA-G2, -10.5, 0.1, 1.0,  -20.5,,
TEMOA-G3, -5.4, 0.2, 1.4,   -2.9,,
TEMOA-G4, -8.9, 0.1, 1.0,   -12.1,,
TEMOA-G5, -1.4, 0.1, 1.0,   -1.8,,
TEETOA-G1, -9.2, 0.1, 1.0,   -0.8,,
TEETOA-G2, -2.3, 0.1, 1.0,   -5.0,,
TEETOA-G3, -7.2, 0.1, 1.0,   -0.8,,
TEETOA-G4, -5.3, 0.1, 1.0,   -5.0,,
TEETOA-G5, -3.2, 0.1, 1.0,   -0.8,,

#
#
# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required.
Participant name:
David Mobley
#
#
# Please list your organization/affiliation, using only UTF-8 characters as described above.
Participant organization:
University of California, Irvine
#
#
# Please provide a brief (40 character limit) informal yet informative name of the method used.
# If using an MD-based method we suggest using the format: Method/EnergyModel/WaterModel/Sampling/[Additional-details-here] , though your name must respect the 40 character limit.
# otherwise you may create your own following the sample text; please edit to your taste.
# The "Name:" keyword is required, as shown here.
# 40 character limit.
Name:
APR/GAFF-RESP/TIP3P/MD-US/NoBuffer_R
#
# All major software packages used and their versions
# Following is sample text; please edit to your taste.
# The "Software:" keyword is required.
Software:
Gromacs 5.0.2
Gaussian 09
#
# Methodology and computational details.
# Level of detail should be at least that used in a publication.
# Please include the values of key parameters, with units, and explain how any
# statistical uncertainties were estimated.
# Use as many lines of text as you need.
# Please explicitly describe how you handle ions (e.g. counterions) and pKa effects
# Following is sample text; please edit to your taste.
# All text following the "Method:" keyword will be regarded as part of your free text methods description.
Method:
All simulations were performed with the pmemd.cuda program from
AMBER14, using our attach-pull-release method (10.1002/jcc.23398,
10.1021/acs.jctc.5b00405). Ten windows were used for the attach phase,
and umbrella sampling windows during the pull phase were spaced at 1
Angstrom intervals, and extended to a maximum distance of 25
Angstroms. As no restraints were added to the host itself, the work of
release could be computed purely analytically.

Each sampling window included a minimum of 50 ns simulation time, with
extension as needed to bring the standard error estimate of the
overall free energy within 0.5 kcal/mol. The longest sampling required
in any window was 125 ns. The bonded and initial Lennard-Jones
parameters were obtained from GAFF. Partial atomic charges were
generated with the RESP procedures as implemented in the program
Antechamber. Sodium or chloride counterions, with parameters from
Joung and Cheatham (10.1021/jp8001614), were added only as needed to
neutralize the total charge of each host-guest system; no additional
counterions were added. The starting structures were obtained by
docking from MOE initially, but were relaxed through short preliminary
MD simulations. Each system was solvated with ~2000 TIP3P waters in an
orthorhombic box whose dimensions were approximately 36 x 36 x 52
cubic Angstroms.

Production simulations were run in the NPT ensemble, with temperature
control using a Langevin thermostat with collision frequency 1.0 ps-1
and pressure control provided by the Monte Carlo barostat. Direct
space nonbonded interactions were truncated with a 9.0 Angstrom cutoff,
whereas long-range electrostatics were handled with the PME method,
using default AMBER settings. SHAKE constraints were applied to bonds
involving hydrogen, and the simulation time step was set to 2 fs.
#
#
# METHOD CATEGORY SECTION
#
# State which method category your prediction method is better described as:
# `Alchemical`, `Quantum`, `Other Physical` `Empirical`, `Mixed`, or `Other`.
# Pick only one category label.
# The `Category:` keyword is required.
Category:
Alchemical
#
# 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