23/09/2013

*** VIRAL CAPSIDS DECOMPOSITIONS INTO QUASI-RIGID DOMAINS ***

Instructions for compiling and running the numerical code.


-Libraries needed:

openmpi
petsc
slepc
boost_program_options


-Untar and make (you will probably need to modify paths/compiler in Makefile):

betaGM-slepc.tar.gz
PiSQRD++-tar.gz
integrity.tar.gz

-Link/copy the executables to an executable path

-Download from viperdb the structure of the full capsid (i.e. 1a34_full.vdb.gz)

-Modify the python script to set the virus name (i.e. 1a34), the number of processors, 
 the number of modes (~100 is usually enough), and the number of proteins in the capsid.

-Run the python script in a folder with the structure file.

-Don't hesitate to contact gpolles@sissa.it for any question or request

NOTE: two of the steps are quite memory intensive. It takes ~20GB of ram for a ~60000 beads
      capsid and ~8GB for a ~40000 one. Structures can be further coarse grained with robust 
      results, but this is not yet automated. Coming soon, though.