ATB and Repository Release Notes ================================== Version 2.1 (29-08-2014) - ATB algorithm: summary of differences between versions 1.2 and 2.1 - Optimized charge group assignment: Canzar S, El-Kebir M, Pool R, Elbassioni K, Malde AK, Mark AE, Geerke DP, Stougie L, Klau GW. Charge Group Partitioning in Biomolecular Simulation. Journal of Computational Biology, 2013, 20, 188-198. - Maximum charge group radius imposed. - Charge group rounding (to an integer) is now only performed if it doesn't cause a large dipole distortion (>1/2 KT) as calculated by the Generalized Born Implicit Solvent model. - Bug fix in charge group transfer from all to united atom topologies. - Fixed oxygen vdw atom type assignment for charged oxygen species. - Topologies compatible with different GROMOS forcefield versions can now be generated, in particular GROMOS 54A7. However, due to the nature of the differences between 53A6 and 54A7 there are only trivial differences in the outputs i.e. different integer parameter codes but the underlying forcefield values are identical. - Bond, angle and dihedral assignment has been modified to not use highly specialized parameters and preference suitable standard forcefield parameters. - Alternative bond, angle and dihedral parameters have been restricted to standard forcefield parameters only. - Improved atom ordering routine has been implemented. - Fix united atom charge group bug caused by modified atom ordering routine. - Use CH2r (type 18) united atom type instead of type CH2 (15) for cyclic carbons. - Repository: summary of differences between versions 1.2 and 2.1 - Structure viewer has been updated to allow for structure type selection e.g. original or optimized geometry. - The ATBs IFP file (in GROMOS++ format) is now compatible with the latest GROMOS package. - "Improper net charge" bug has been fixed. - JME has been switched for JSME. - JMol has been switched for JSMol. - Improved error handling for website and ATB computation pipeline. - Calculated force constants for radical species or transition states will no longer be included in the ATB's IFP file. - Removed underscore from RNME generation. - FAQ should now be more informative. - An automated Thermodynamic Integration solvation free energy pipeline has been added (usage is currently restricted to approved users).