PRACE/BioExcel Seasonal School 2019 - AMBER HANDS ON ANALYSIS SESSION

Thomas E. Cheatham III, Christina Bergonzo, Daniel Roe, & Rodrigo Galindo-Murillo

...with links to the official AMBER tutorials and also tutorials on the AmberHub...

There are a variety of sources for AMBER tutorials, the official ones from ambermd.org, a set of CPPTRAJ rich ones from AmberHub @ CHPC, and a set of tutorials updated from AMBER London 2015 and PRACE/BioExcel 2017 linked below.

• Note: You will want to load the latest module for AMBER on beskow.

  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 tegner.

• 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

• AMBER CPPTRAJ tutorial 0 from ambermd.org - Basics and interactive use of CPPTRAJ

• AMBER CPPTRAJ tutorial 1 from ambermd.org - RMSD fitting and fits to reference structures that may have a different number of atoms or topology

• DNA-tutorial with some additional basic analyses

• Principal component analysis

• Cluster and combined cluster analysis

• Hydrogen bond analysis

• Replica exchange analysis

Copyright Thomas E. Cheatham III, Christina Bergonzo, Daniel Roe & Rodrigo Galindo-Murillo, 2015