Protein Preparation Wizard

The Protein Preparation Wizard allows you to take a protein from its raw state, (which may be missing hydrogen atoms and have incorrect bond order assignments, charge states, or orientations of various groups) to a state in which it is properly prepared for calculations using Schrödinger products such as Glide, Prime, QSite, Liaison, and MacroModel.
Note: Distributed jobs can only be carried out if input is Maestro type, please enter the number of jobs to run on the specified host and number of processors.

Backend implementation

Options

Column containing structures

Column in the input data table containing the protein structures.

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaces Input - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Assign bond orders

Assign bond orders to het groups.

Add hydrogens

Add hydrogens to the structure.

Treat metals

Break bonds to metals and correct formal charges to metals and neighboring atoms.

Selenomethionines

Convert Selenomethionine residues to Methionines.

Treat disulfides

Create bonds to proximal Sulfurs (delete hydrogens as needed).

Delete waters

Delete waters #A from het groups (default is 5).

Fill loops

Fill in missing loops from the SEQRES records in the PDB file, using Prime. The input PDB structure can be in either PDB or Maestro format.

Cap termini

Add ACE (N-acetyl)and NMA (N-methyl amide) groups to N and C termini.

Sample water orientations

ProtAssign: sample waters.

Minimize to RMSD

Run Glide protein prep, constrained refinement (Impref) using the RMSD cutoff (default is 0.3).

Hydrogens only

Impref: Fix heavy atoms (minimize hydrogens only).

Number of subjobs

If not selected, total number of processors will be used as subjobs count

Parameter flow variables

Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: PrepWizard
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option from command line, just specify the option_name and the value as _off_ through the flow variable.

Views

Log output

Log output

Workflows

• Binding site 1KNIME Hub
• Binding site 1-2KNIME Hub
• Binding site 1-3KNIME Hub
• Binding site shape clusteringKNIME Hub
• Binding site shape clusteringKNIME Hub
• Show all 71 workflows

Links

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Developers