Haddock Multi form tool

Haddock Multi Form Tool: Single Run Settings

Reload single settings: | |||||

Name | You may supply a name for your docking run (one word) |
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1. Mol structure file: | 2. Mol structure file: | 3. Mol structure file: | |||

4. Mol structure file: | 5. Mol structure file: | 6. Mol structure file: | |||

TBL file(ambiguous restraints) | TBL file(unambiguous restraints) | ||||

Username |
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Password |
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Molecules definition

First molecule

Structure definition | |

Where is the structure provided? Possible choices: submit download (Please seperate by comma only e.g. submit,download) | |

Which chain of the structure must be used? Possible choices: Char "A" to "Z" or "All" (Please seperate by comma only e.g. A,B,C) | |

PDB structure to submit | |

or: PDB code to download | |

Segment ID to use during the docking | |

What kind of molecule are you docking? Possible choices: Protein, Protein-DNA, Protein-RNA, DNA or RNA (Please seperate by comma only e.g. Protein,Protein-DNA,Protein-RNA) |

Histidine protonation states

Automatically guess histidine protonation states using molprobity | |

Histidines | |

First histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Second histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Third histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fourth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fifth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Sixth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Seventh histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Eighth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Ninth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Tenth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) |

Semi-flexible segments

Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement | |

How are the flexible segments defined? Possible choices: manual, automatic, full, none | |

Semi-flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number | |

Sixth segment | |

First number | |

Last number | |

Seventh segment | |

First number | |

Last number | |

Eighth segment | |

First number | |

Last number | |

Ninth segment | |

First number | |

Last number | |

Tenth segment | |

First number | |

Last number |

Fully flexible segments

These segments will be allowed to move at all stages of it1 | |

Fully flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number |

The N-terminus of your protein is positively charged | |

The C-terminus of your protein is negatively charged |

Second molecule

Structure definition | |

Where is the structure provided? Possible choices: submit download (Please seperate by comma only e.g. submit,download) | |

Which chain of the structure must be used? Possible choices: Char "A" to "Z" or "All" (Please seperate by comma only e.g. A,B,C) | |

PDB structure to submit | |

or: PDB code to download | |

Segment ID to use during the docking | |

What kind of molecule are you docking? Possible choices: Protein, Protein-DNA, Protein-RNA, DNA or RNA (Please seperate by comma only e.g. Protein,Protein-DNA,Protein-RNA) |

Histidine protonation states

Automatically guess histidine protonation states using molprobity | |

Histidines | |

First histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Second histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Third histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fourth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fifth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Sixth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Seventh histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Eighth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Ninth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Tenth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) |

Semi-flexible segments

Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement | |

How are the flexible segments defined? Possible choices: manual, automatic, full, none | |

Semi-flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number | |

Sixth segment | |

First number | |

Last number | |

Seventh segment | |

First number | |

Last number | |

Eighth segment | |

First number | |

Last number | |

Ninth segment | |

First number | |

Last number | |

Tenth segment | |

First number | |

Last number |

Fully flexible segments

These segments will be allowed to move at all stages of it1 | |

Fully flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number |

The N-terminus of your protein is positively charged | |

The C-terminus of your protein is negatively charged |

Third molecule

Structure definition | |

Where is the structure provided? Possible choices: submit download (Please seperate by comma only e.g. submit,download) | |

Which chain of the structure must be used? Possible choices: Char "A" to "Z" or "All" (Please seperate by comma only e.g. A,B,C) | |

PDB structure to submit | |

or: PDB code to download | |

Segment ID to use during the docking | |

What kind of molecule are you docking? Possible choices: Protein, Protein-DNA, Protein-RNA, DNA or RNA (Please seperate by comma only e.g. Protein,Protein-DNA,Protein-RNA) |

Histidine protonation states

Automatically guess histidine protonation states using molprobity | |

Histidines | |

First histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Second histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Third histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fourth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fifth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Sixth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Seventh histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Eighth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Ninth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Tenth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) |

Semi-flexible segments

Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement | |

How are the flexible segments defined? Possible choices: manual, automatic, full, none | |

Semi-flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number | |

Sixth segment | |

First number | |

Last number | |

Seventh segment | |

First number | |

Last number | |

Eighth segment | |

First number | |

Last number | |

Ninth segment | |

First number | |

Last number | |

Tenth segment | |

First number | |

Last number |

Fully flexible segments

These segments will be allowed to move at all stages of it1 | |

Fully flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number |

The N-terminus of your protein is positively charged | |

The C-terminus of your protein is negatively charged |

Fourth molecule

Structure definition | |

PDB structure to submit | |

or: PDB code to download | |

Segment ID to use during the docking | |

Histidine protonation states

Automatically guess histidine protonation states using molprobity | |

Histidines | |

First histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Second histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Third histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fourth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fifth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Sixth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Seventh histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Eighth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Ninth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Tenth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) |

Semi-flexible segments

Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement | |

How are the flexible segments defined? Possible choices: manual, automatic, full, none | |

Semi-flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number | |

Sixth segment | |

First number | |

Last number | |

Seventh segment | |

First number | |

Last number | |

Eighth segment | |

First number | |

Last number | |

Ninth segment | |

First number | |

Last number | |

Tenth segment | |

First number | |

Last number |

Fully flexible segments

These segments will be allowed to move at all stages of it1 | |

Fully flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number |

The N-terminus of your protein is positively charged | |

The C-terminus of your protein is negatively charged |

Fifth molecule

Structure definition | |

PDB structure to submit | |

or: PDB code to download | |

Segment ID to use during the docking | |

Histidine protonation states

Automatically guess histidine protonation states using molprobity | |

Histidines | |

First histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Second histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Third histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fourth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fifth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Sixth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Seventh histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Eighth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Ninth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Tenth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) |

Semi-flexible segments

Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement | |

How are the flexible segments defined? Possible choices: manual, automatic, full, none | |

Semi-flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number | |

Sixth segment | |

First number | |

Last number | |

Seventh segment | |

First number | |

Last number | |

Eighth segment | |

First number | |

Last number | |

Ninth segment | |

First number | |

Last number | |

Tenth segment | |

First number | |

Last number |

Fully flexible segments

These segments will be allowed to move at all stages of it1 | |

Fully flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number |

The N-terminus of your protein is positively charged | |

The C-terminus of your protein is negatively charged |

Sixth molecule

Structure definition | |

PDB structure to submit | |

or: PDB code to download | |

Segment ID to use during the docking | |

Histidine protonation states

Automatically guess histidine protonation states using molprobity | |

Histidines | |

First histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Second histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Third histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fourth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Fifth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Sixth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Seventh histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Eighth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Ninth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) | |

Tenth histidine | |

Residue number | |

Protonation state. Possible choices: HISD,HISE,HIS+ (Please seperate by comma only e.g. HISD,HISE) |

Semi-flexible segments

Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement | |

How are the flexible segments defined? Possible choices: manual, automatic, full, none | |

Semi-flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number | |

Sixth segment | |

First number | |

Last number | |

Seventh segment | |

First number | |

Last number | |

Eighth segment | |

First number | |

Last number | |

Ninth segment | |

First number | |

Last number | |

Tenth segment | |

First number | |

Last number |

Fully flexible segments

These segments will be allowed to move at all stages of it1 | |

Fully flexible segments | |

First segment | |

First number | |

Last number | |

Second segment | |

First number | |

Last number | |

Third segment | |

First number | |

Last number | |

Fourth segment | |

First number | |

Last number | |

Fifth segment | |

First number | |

Last number |

The N-terminus of your protein is positively charged | |

The C-terminus of your protein is negatively charged |

Molecule interaction matrix

Mol 1 | |

Mol 1 1 | |

Mol 1 2 | |

Mol 1 3 | |

Mol 1 4 | |

Mol 1 5 | |

Mol 1 6 | |

Mol 2 | |

Mol 2 1 | |

Mol 2 2 | |

Mol 2 3 | |

Mol 2 4 | |

Mol 2 5 | |

Mol 3 | |

Mol 3 1 | |

Mol 3 2 | |

Mol 3 3 | |

Mol 3 4 | |

Mol 4 | |

Mol 4 1 | |

Mol 4 2 | |

Mol 4 3 | |

Mol 5 | |

Mol 5 1 | |

Mol 5 2 | |

Mol 6 | |

Mol 6 1 |

Distance restraints

If you specified that passive residues will be defined automatically, all surface residues will be selected within the following radius (in angstroms) around the active residues | |

Instead of specifying active and passive residues, you can supply a HADDOCK restraints TBL file (ambiguous restraints) | |

You can supply a HADDOCK restraints TBL file with restraints that will always be enforced (unambiguous restraints) | |

If one of your molecules is DNA/RNA, restraints are automatically created to preserve its structure. | |

Uncheck this option if you are docking with unstructured DNA/RNA | |

Create DNA/RNA restraints? | |

HADDOCK deletes by default all hydrogens except those bonded to a polar atom (N, O). | |

Uncheck this option if you have NOEs or other specific restraints to non-polar hydrogens | |

Remove non-polar hydrogens? | |

Random patches | |

Define randomly ambiguous interaction restraints from accessible residues | |

Center of mass restraints | |

Define center of mass restraints to enforce contact between the molecules | |

Force constant for center of mass contact restraints | |

Surface contact restraints | |

Define surface contact restraints to enforce contact between the molecules | |

Force constant for surface contact restraints | |

Random exclusion | |

Randomly exclude a fraction of the ambiguous restraints (AIRs) | |

Number of partitions for random exclusion (%excluded=100/number of partitions) | |

Do you want to define a radius of gyration restraint (e.g from SAXS)? | |

Radius of gyration |

Sampling parameters

Number of structures for rigid body docking | |

Number of trials for rigid body minimisation | |

Sample 180 degrees rotated solutions during rigid body EM | |

Number of structures for semi-flexible refinement | |

Sample 180 degrees rotated solutions during semi-flexible SA | |

Solvent to use for the last iteration. Possible choice: water or dmso | |

Number of structures for the explicit solvent refinement | |

Epsilon constant for the electrostatic energy term | |

Note that for explicit solvent refinement cdie with epsilon=1 is used | |

Epsilon | |

Solvated docking mode | |

Perform solvated docking |

Parameters for clustering

Clustering method (RMSD or Fraction of Common Contacts (FCC)). Possible choice RMSD or FCC | |

RMSD Cutoff for clustering (Recommended: 7.5A for RMSD, 0.6 for FCC for multimers) | |

Minimum cluster size | |

Chain-Agnostic Algorithm (used for FCC clustering in symmetrical complexes) | |

fcc_ignc |

Dihedral and hydrogen bond restraints

In addition to distance restraints, you may specify dihedral and hydrogen bond restraints | |

These restraints can be inter- or intramolecular | |

Dihedral angle restraints TBL file | |

Hydrogen bond restraints TBL file |

Noncrystallographic symmetry restraints

NCS parameters | |

Use this type of restraints | |

Force constant |

Segment pair

Segment pair 1

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

Segment pair 2

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

Segment pair 3

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

Segment pair 4

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

Segment pair 5

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

Symmetry restraints

Symmetry parameters | |

Use this type of restraints | |

Force constant |

C2 symmetry segment pair

C2 symmetry segment pair 1

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 2

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 3

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 4

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 5

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 6

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 7

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 8

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 9

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C2 symmetry segment pair 10

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C3 symmetry segment triple

C3 symmetry segment triple 1

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 3 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C3 symmetry segment triple 2

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 3 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C4 symmetry segment quadruple

C4 symmetry segment quadruple 1

Segment | |

Segment 0 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 3 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C4 symmetry segment quadruple 2

Segment | |

Segment 0 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 3 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

C5 symmetry segment quintuple

C5 symmetry segment quintuple 1

Segment | |

Segment 1 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 2 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 3 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 4 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty | |

Segment 5 | |

First number | |

Last number | |

Segment ID. Possible choice: All, A-Z or leave empty |

Restraints energy constants

Energy constants for unambiguous restraints

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Energy constants for ambiguous restraints

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Energy constants for hydrogen bond restraints

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Energy constants for dihedral angle restraints | |

hot | |

cool1 | |

cool2 | |

cool3 | |

Automatically define backbone dihedral restraints from structure? Possible choice: none,all,alpha or alphabeta | |

Energy constants for radius-of-gyration restraints | |

hot | |

cool1 | |

cool2 | |

cool3 | |

Atom selections for the radius of gyration restraint. Possible choice: all or leave field empty |

Residual dipolar couplings

Residual dipolar couplings 1

RDC type. Possible choice: NO,SANI,XRDC or VANGLE | |

R | |

D |

SANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

VEAN energy constants

ini_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

ini_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

HADDOCK TBL file containing RDC restraints | |

RDC file |

Residual dipolar couplings 2

RDC type. Possible choice: NO,SANI,XRDC or VANGLE | |

R | |

D |

SANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

VEAN energy constants

ini_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

ini_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

HADDOCK TBL file containing RDC restraints | |

RDC file |

Residual dipolar couplings 3

RDC type. Possible choice: NO,SANI,XRDC or VANGLE | |

R | |

D |

SANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

VEAN energy constants

ini_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

ini_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

HADDOCK TBL file containing RDC restraints | |

RDC file |

Residual dipolar couplings 4

RDC type. Possible choice: NO,SANI,XRDC or VANGLE | |

R | |

D |

SANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

VEAN energy constants

ini_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

ini_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

HADDOCK TBL file containing RDC restraints | |

RDC file |

Residual dipolar couplings 5

RDC type. Possible choice: NO,SANI,XRDC or VANGLE | |

R | |

D |

SANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

VEAN energy constants

ini_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_bor energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

ini_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 | |

fin_cen energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

HADDOCK TBL file containing RDC restraints | |

RDC file |

Pseudo Contact Shifts restraints

Tensor distance restraints file for all PCS restraints |

PCS restraints 1

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 2

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 3

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 4

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 5

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 6

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 7

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 8

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 9

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

PCS restraints 10

PCS type. Possible choice: NO or XPCS |

PCS energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

R | |

D | |

PCS file |

Relaxation anisotropy restraints

Anisotropy restraints 1

Anisotropy type. Possible choice: NO or DANI |

DANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Correlation time | |

D | |

R | |

H frequency | |

N frequency | |

Anisotropy file |

Anisotropy restraints 2

Anisotropy type. Possible choice: NO or DANI |

DANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Correlation time | |

D | |

R | |

H frequency | |

N frequency | |

Anisotropy file |

Anisotropy restraints 3

Anisotropy type. Possible choice: NO or DANI |

DANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Correlation time | |

D | |

R | |

H frequency | |

N frequency | |

Anisotropy file |

Anisotropy restraints 4

Anisotropy type. Possible choice: NO or DANI |

DANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Correlation time | |

D | |

R | |

H frequency | |

N frequency | |

Anisotropy file |

Anisotropy restraints 5

Anisotropy type. Possible choice: NO or DANI |

DANI energy constants

Iterations: | |

0: Rigid body EM (it0) | |

1: Semi-flexible SA (it1) | |

2: Water refinement | |

First iteration (0-2) | |

Last iteration (0-2) | |

Energy constants per stage | |

hot | |

cool1 | |

cool2 | |

cool3 |

Correlation time | |

D | |

R | |

H frequency | |

N frequency | |

Anisotropy file |

Energy and interaction parameters

Nonbonded parameters. Possible choice: PROLSQ, PARMALLH6, PARALLHDG or OPLSX | |

Do you want to include dihedral angle energy terms? | |

These are independent of dihedral angle restraints | |

Include dihedral angle restraints | |

Do you want to include the electrostatic energy term for docking? | |

Note that it will be automatically included in the solvent refinement | |

Include electrostatic during rigid body docking (it0) | |

Include electrostatic during semi-flexible SA (it1) | |

Use constant (cdie) or distance-dependent (rdie) dielectric | |

Scaling of intermolecular interactions for rigid body EM | |

Scaling of intermolecular interactions for semi-flexible SA (it1) | |

Initial value | |

Rigid body dynamic | |

SA with flexible side-chains (cool2) | |

SA with flexible backbone and side-chains (cool3) | |

Final value | |

Rigid body dynamic | |

SA with flexible side-chains (cool2) | |

SA with flexible backbone and side-chains (cool3) |

Scoring parameters

Define the weights for the various terms for the sorting of structures (scoring) | |

1: Rigid body EM (it0) | |

2: semi-flexible SA (it1) | |

3: water refinement | |

Evdw | |

Evdw 1 | |

Evdw 2 | |

Evdw 3 | |

Eelec | |

Eelec 1 | |

Eelec 2 | |

Eelec 3 | |

Eair | |

Eair 1 | |

Eair 2 | |

Eair 3 | |

Erg | |

Erg 1 | |

Erg 2 | |

Erg 3 | |

Esani | |

Esani 1 | |

Esani 2 | |

Esani 3 | |

Exrdc | |

Exrdc 1 | |

Exrdc 2 | |

Exrdc 3 | |

Expcs | |

Expcs 1 | |

Expcs 2 | |

Expcs 3 | |

Edani | |

Edani 1 | |

Edani 2 | |

Edani 3 | |

Evean | |

Evean 1 | |

Evean 2 | |

Evean 3 | |

Ecdih | |

Ecdih 1 | |

Ecdih 2 | |

Ecdih 3 | |

Esym | |

Esym 1 | |

Esym 2 | |

Esym 3 | |

BSA | |

BSA 1 | |

BSA 2 | |

BSA 3 | |

dEint | |

dEint 1 | |

dEint 2 | |

dEint 3 | |

Edesolv | |

Edesolv 1 | |

Edesolv 2 | |

Edesolv 3 |

Advanced sampling parameters

Do you want to cross-dock all combinations in the ensembles of starting structures? | |

Turn off this option if you only want to dock structure 1 of ensemble A | |

to structure 1 of ensemble B, structure 2 to structure 2, etc. | |

Perform cross-docking | |

Enable this option to multiply the number of structures in all iterations by the number of starting structure combinations. | |

The number of combinations depends on the cross-docking parameter. | |

If cross-docking is disabled, the number of combinations is the size of the first ensemble. | |

If cross-docking is enabled, the number of combinations is the sizes of all ensembles multiplied. | |

Multiply the number of calculated structures by all combinations | |

Randomize starting orientations | |

Perform initial rigid body minimisation | |

Allow translation in rigid body minimisation | |

initial seed for random number generator | |

it1 parameters | |

temperature for rigid body high temperature TAD | |

initial temperature for rigid body first TAD cooling step | |

final temperature after first cooling step | |

initial temperature for second TAD cooling step with flexible side-chain at the inferface | |

final temperature after second cooling step | |

initial temperature for third TAD cooling step with fully flexible interface | |

final temperature after third cooling step | |

time step | |

factor for timestep in TAD | |

number of MD steps for rigid body high temperature TAD | |

number of MD steps during first rigid body cooling stage | |

number of MD steps during second cooling stage with flexible side-chains at interface | |

number of MD steps during third cooling stage with fully flexible interface | |

final solvated refinement | |

number of steps for heating phase (100, 200, 300K) | |

number of steps for 300K phase | |

number of steps for cooling phase (300, 200, 100K) | |

calculate explicit desolvation energy (note this will double the cpu requirements) |

Solvated docking parameters

Solvated docking can be enabled in the Sampling Parameters section | |

Which method to use for solvating? | |

db: database-based (recommended), restraints: for restrained solvating to amino-acid most often forming | |

Method. db or restraints | |

Which propensity database to use? | |

Statistical: based on an analysis of water-mediated contacts in the PDB, Kyte-Doolittle: based on the Kyte-Doolittle hydrophobicity scale | |

Database method. statistical or kytedoolittle | |

Initial cutoff for restraints solvating method | |

Cutoff for restraints solvating method | |

Scale factor for restraints solvating method | |

This is the fraction of all interface water after the initial rigid body docking that will be kept (note that more waters might be removed if the interaction energy is unfavorable) | |

Fraction of water to keep in ntrial loop | |

This is the fraction of interface water involving DNA phosphates after the initial rigid body docking that will be kept (note that more waters might be removed if the interaction energy is unfavorable) | |

Fraction of water to keep in ntrial loop for DNA phosphates | |

Additional random fraction of water to keep in ntrial loop | |

Water-surface-cutoff | |

Do some water analysis | |

Use translation in loop miniwater | |

How many different solvation shells to generate |

Analysis parameters

Number of structures to analyze | |

Cutoff distance (proton-acceptor) to define an hydrogen bond | |

Cutoff distance (carbon-carbon) to define an hydrophobic contact | |

After the final solvent refinement, write additional PDB files including solvent |