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This is an upgraded version (4.0) of H++. This release includes the following upgrades:

This is the upgraded (3.2) version of H++. The main changes relative to the previous release (3.1) are summarized below:

1. Most common ions can now be retained for pK calculations and will be included in the output topology/parameter and coordinate files. See FAQ for details.

2. H++ now uses the latest version of AmberTools and Amber force field parameters: AmberTools 15 using ff14SB force field parameters for proteins. with OL3 modifications for RNA, and OL1+OL4 modifications for DNA. See FAQ for details.

3. Water model option for solvent box. When generating an explicit solvent box, you can now select between two types of water models: OPC, a highly accurate 4-point water model, and TIP3P, the traditional 3-point water model. See [Izadi et. al., 2015, J Phys Chem Lett, 5(21), 3863-3871] for additional information on OPC.
This is the upgraded (3.1) version of H++. The main changes relative to the previous release (3.0) are summarized below:

1. The default value of internal dielectric has been changed to 10.0, which on average improves the accuracy of pK calculations; click here for more details.

The 3.0 version of H++ released on 5/2011 is described in R. Anandakrishnan, B. Aguilar and A. V. Onufriev, Nucleic Acids Res., 40(W1):W537-541. (2012). The main changes relative to the previous release (2.0) are summarized below:

1. H++ now runs on a faster server machine which reduced the processing time by several times.

2. The GB option for electrostatic calculation has been removed.

3. Implemented "reduce" to protonate and improve input structure

4. H++ now uses Amber11 and MEAD 2.2.9.

5. Several bugs fixed.

The main changes introduced in version 2.0 (released in 6/2010) relative to the original (1.0) release are summarized below:

1. Ability to automatically process non-protein ligands has been added.

2. Ability to automatically process DNA and RNA, whether as a ligand or as a stand-alone structure. When no titratable site are found, the PQR (and AMBER topology/coordinate) files are still generated.

3. Registered users now have access to all runs, including the failed ones. A master log file containing all major warning/error messages is now available.

4. Total charge at the user specified pH is now reported.

5. Separate output option for AMBER explicit solvent box (no box by default)i has been added.

6. Total charge is now reported on the titration curve.

7. Several minor bugs fixed.