FreeSolv Versions Save

• Remove redundant molecule mobley_4689084 (which duplicates mobley_352111 , had the same experimental value, and a calculated value within uncertainty)
• Add utility functionality to easily check for duplicates; rebuild database after removing above duplicate and checking for others
• Update reference for calculated values to refer to the J Chem Engr Data reference.

These changes were made to the repo some eight months ago but apparently I forgot to make a new release at that time.

• Introduces automatically-generated input files for CHARMM, DESMOND, and LAMMPS, and alternate GROMACS files generated via ParmEd rather than acpype
• Reorganizes (renames) directories containing input files for simulations
• Provides energy comparison of all automatically generated files in simulation_comparison_input
• Adds of notebooks directory with IPython notebook which can generate input for hydration calculations on OpenEye platforms like Orion

This version provides a full rebuild of the input files for the FreeSolv database, and also updates all calculated values via a fresh set of calculations, as further discussed in https://github.com/MobleyLab/FreeSolv/pull/28 and in a paper submitted to the Journal of Chemical and Engineering Data (a link to a preprint will be posted in the README.md as soon as it is available). Additional calculated values are added, such as enthalpies of hydration and electrostatic and nonpolar components of the hydration free energy.

This update remedies problems with earlier versions of the database where (for example) some topology files contained water molecules whereas others did not, etc. These issues were present since input files were pulled together from a variety of separate studies conducted over a number of years with somewhat different protocols. This update ensures all input files are generated at one time using a consistent protocol, and provides a script to use re-generating the input files in future updates.

Same as version 0.32; used to trigger an initial Zenodo release/DOI now that I have turned on Zenodo integration.

• Corrected SMILES strings (and other files) for nitro-containing compounds mobley_3802803 and mobley_9741965. Due to some type of earlier error, the GAFF and SYBYL .mol2 files for these contained incorrect bonding in the nitro group(s), which resulted in generation of incorrect SMILES when generating FreeSolv. These SMILES strings have now been corrected, as has the bond type in the .mol2 files. Partial charges in the topology files and .mol2 files were retained as use for the calculations reported here, and will be updated in a subsequent release when the calculations are repeated. Checkmol groups for these compounds were also updated. Thanks to Christopher Bayly for noticing these issues. (9/29/15)
• Added (temporarily?) unique, short nicknames to all compounds in database.txt and database.pickle; these consist of IUPAC names when short, or common/other names which are unique and lead to useful hits when used as search terms. (Approx. 10/21/14)
• Removed mobley_4689084, which duplicates mobley_352111 (same experimental value and source data, but the calculated value of the former is older, and topology/coordinate file were less well curated). (10/24/14)

This version of FreeSolv v0.31 was posted on the UCI escholarship site on 25 Sep 2014:

http://www.escholarship.org/uc/item/6sd403pz