PRACE/BioExcel Seasonal School 2019 - AMBER HANDS ON ANALYSIS SESSIONThomas E. Cheatham III, Christina Bergonzo, Daniel Roe, & Rodrigo Galindo-Murillo
...with links to the official AMBER tutorials and also tutorials on the AmberHub...
- Note: You will want to load the latest module for AMBER on
module load amber/18.ambertools.19
- If you are on beskow and type cpptraj and you get "Illegal Instruction" you are
running on the front-end node (which has a different
architecture). You will need to either submit commands as batch or
get a pseudo-interactive session via salloc.
- salloc -A edu19.bioexcel -t "time in minutes" --reservation "reservation"
- To show active reservations, scontrol show
- On beskow there are not true interactive sessions, only batch, so
you cannot run cpptraj interactively; if you want to do this, use
- The back-end nodes where things are running do not access AFS, so
work out of your scratch directory; cd /cfs/scratch/X/username where
X is the first letter (lowercase) of your name.
- If you run cpptraj interactively, it will accept commands you type
but not actually process anything until end-of-file is specified
which will run the program and then terminate, so better off running
in traditional batch mode... (i.e. edit an input file with the
commands and run it as cpptraj -i "my inout file name".
- I suggest you "read" about the CPPTRAJ interactive usage, and then follow the instructions for running in batch which is more typical.
Basic analysis tutorials from the AMBER London 2015 Workshop
Copyright Thomas E. Cheatham III, Christina Bergonzo, Daniel Roe & Rodrigo Galindo-Murillo, 2015