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fixpka - pKa Normalization

fixpka has a rule-based system to set the ionization state of input molecules. If pKa normalization is turned on, the molecule is set to its most energetically favorable ionization state for pH=7.4. The rule-based nature of this calculation allows it to be very fast. Further, despite being rule-based, this approach takes into account many secondary charge interactions.

While more advanced levels of theory can be found for predicting ionization states, this method is very well suited to virtual-screening database preparation. However, fixpka may not be appropriate for hit-to-lead or lead optimization.

fixpka Usage

Required Parameters

-in

File containing one or more molecules from which pKa normalization will be done. An input file is required, but the -in flag is optional. The first parameter listed with no flag will be automatically mapped to the input file. Unflagged parameters must occur last in the parameter list. Any OpenEye supported molecule format can be used for input.

-out

File for writing output. An output file is required, but the -out flag is optional. The second parameter listed with no flag will be automatically mapped to the input file. Unflagged parameters must occur last in the parameter list. Any OpenEye supported molecule format can be used for output but .smi or .ism is recommended.

Optional parameters

-ionize

Specifies ionization environment, either neutral pH or un-ionize, to remove all ions possible. Legal values are neutral, 7.4, un-ionize, and unionize.

Example Commands

The following section shows a common command-line execution of fixpka.

prompt> fixpka drugs.sdf fixpka_drugs.smi

Reads the file drugs.sdf in SD format, sets the pKa state of each molecule and writes them into the file fixpka_drugs.smi.