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 email@example.com
(or firstname.lastname@example.org if you want a general discussion).
- Selected responses from the Amber Reflector
- Installation and Compilation questions
- Structure building
- Molecular Dynamics and Minimization questions (sander/gibbs)
- Analysis Questions
- 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 lastist in get_istack
I keep getting linmin failures with minimization...
- Machine precision:
How come my results are different on different machines?
- Parm complains about
- PBC restraints:
Some notes on NMR distance restraints with
periodic boundary conditions...
- Parameters and representations...
What units are charges, velocities etc. in
- Force fields:
How parameters were derived
What are the various types of histidine residues
represented in AMBER?
Are there any parameters for carbohydrate within AMBER?
- OPLS questions
- Neutral ASP, GLU:
How to get the H in the COOH?
Are there any fluorine parameters for AMBER?
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...
how they are defined and why.
Miscellaneous parameters from the literature.