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).


You do not need to provide an email adress, a link to the results will be returned. If you provide an email address, a link to the results will be sent to this address. Please make sure that the email address is correct.


SAMPLE RUN: Please, click here.

QUESTIONS? Please, have a look here.

Need help with parameters? Click here.

SUPPORT:
For questions, please do not hesitate to contact support[at]nmsim.de.












Version 2.0