Normal mode-based geometric simulation

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PDB ID
 		 OR    *
Type of simulation: Small scale motions
(loops, docking ensembles, distinct starting structures)

Large scale motions
(opening and closing of domains)

Radius of gyration-guided motions
(biased simulation towards lower (or larger) ROG)

Targeted simulation
Target PDB-File  *
Rigid cluster decomposition parameters (FIRST): E-cutoff for H-bonds

Hydrophobic method

  Hydrophobic cutoff
Normal mode parameters (RCNMA): RCNMA  ENM    Cutoff for C-alpha atoms
Simulation
parameters (NMSim): 		No. of trajectories

No. of NMSim cycles

Side-chain distortions

Step size

  No. of sim. cycles

  Output frequency

  NM mode range          1-

  ROG mode

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 © CPC lab, 2011












*PLEASE NOTE:

Alternative sidechain conformations are not allowed.

The PDB file must not be larger than 5000 atoms.

Structural preparation before simulation:

 - Incomplete residues will be fixed.

 - Waters and ligands will be removed.

 - Hydrogens will be added (are not required for input PDB file).


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Version 2.0