AMBER FAQ (Frequently Asked Questions)

This list of questions, problems, answers and opinions has been developed over the years based on user questions and discussions on the Amber Mail Reflector. http://archive.ambermd.org/
If you have any suggestions to improve these answers, please send them to amber-admin@biomaps.rutgers.edu (or amber@ambermd.org if you want a general discussion).

• Selected responses from the Amber Reflector

• Installation and Compilation questions
  • Some parameter is too small (or can't get memory)

• Structure building
  • Resp charge-fitting topics
  • LEaP
    • Some general LEaP questions
    • Non-aqueous solvent: How can one set up a non-aqueous solvent box in AMBER?
    • xLEaP Problems
  • Generating helices: How do we generate alpha-helices, etc with AMBER?
  • Nucleic acids: Common problems

• Molecular Dynamics and Minimization questions (sander/gibbs)
  • Energy minimization
  • Equilibration: E.g. how does one equilibrate a solvated system?
  • Periodic Boundary: What should the output look like?
  • Nonperiodic/vacuum
  • Constant Pressure: Shouldn't my pressure stabilize at exactly 1.0 atm?
  • Ewald
  • Polarization
  • Sander/Gibbs crash w/ lots of atoms
  • Constraints and restraints
  • Dielectric constant: What dielectric does one use with water?
  • Belly: Why does my solute move when belly is used w/ constant pressure?
  • Dynamics: restarting..
  • Docking: Can one perform ``docking'' with sander?
  • Free energy / gibbs questions
  • NMR topics...

• Analysis Questions
  • Coordinate/trajectory analysis
  • Carnal
  • Nmode: Are the modes produced by NMODE (mass-)normalized?
    Are frequencies themselves output, or their squares?
    

• Common failures...
  • BLOWUP: Many users experience seemingly random SHAKE failures and/or problems when starting a periodic boundary simulation where the boxs expands initially. Signs of shake failure are the error message: COORDINATE RESETTING CANNOT BE ACCOMPLISHED.
  • EWALD BOMBs are of several types: Non bond list overflow
    See the Selected reponses from the Amber mail reflector.
  • Exceeding: Exceeding lastist in get_istack
    Exceeding lastrst
  • Gibbs.
  • LINMIN: I keep getting linmin failures with minimization...
  • Machine precision: How come my results are different on different machines?
  • Parm complains about missing parameters.
  • PBC restraints: Some notes on NMR distance restraints with periodic boundary conditions...
  • Sander.
  • Water.

• Parameters and representations...
  • Units: What units are charges, velocities etc. in various files?
  • Force fields: How parameters were derived
  • Histidine: What are the various types of histidine residues represented in AMBER?
  • Carbohydrates: Are there any parameters for carbohydrate within AMBER?
  • OPLS questions
  • Neutral ASP, GLU: How to get the H in the COOH?
  • Fluorine: Are there any fluorine parameters for AMBER?
  • Sulfur: Where can I obtain sulfur-related parameters?
  • Van der Waals: How do the prmtop ACOEFF and BCOEFF relate to the common formulation of the van der Waals equation? (pdf file!)
  • Van der Waals: Tell me about AMBER Van der Waals parameters, e.g. adding new ions...
  • Angle params: 5-membered ring parameters seem wrong...
  • Impropers: how they are defined and why.
  • Parameters: Miscellaneous parameters from the literature.

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