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H++ is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H++

If this is your first time using H++, please read the FAQ carefully.

H++ in more detail. Citations

Please report problems to the H++ team: ramu@vt.edu


8/2022 - AMBER compatible output PDB structure includes CONECT records

1/2022 - New release of H++ (Version 4.0), which includes the following upgrades: 7/2019 - H++ can now process structures with phosphorylated side chains. See FAQ.

7/2019 - FAQ has been updated to indicate that the c-terminus can be capped with an amide cap (-NH2), in addition to N-methylamide (NME) capping.

11/2018 - Fixed error encountered when processing a structure containing more than two CYS residues within 3A of each other.

11/2017 - Security and operating system upgrade to prevent unauthorized access to the H++ server

12/2016 - H++ can now calculate the pKs for proteins embedded in a membrane. See FAQ for details.

NOTE: Current AMBER force fields in use: ff19SB for protein, ff99bsc0+bsc1 for DNA, ff99bsc0_CaseP_Shaw for RNA, lipid17 for lipids, ionsjc_tip4pew+ions234lm_126_tip4pew for ions) See FAQ for details.