Equilibration of solvated protein: protein-generate_solvate.inp

The example needs the histidine patch as described in setup/titratable  so fsc-generate_solvate.inp contains the patch.

Parameters to charmm:

parameters options default
pdbfile= root of pdbfile name also segid of protein none, die
toppar= path to topology and parameter files $toppar
crystal= true, false false
shape= cubic, octahedral cubic
solvate= true, false none, die

Required files and directories:

Build and minimize in vacuum:

% setenv toppar = "."
% charmm pdbfile=1fsc < fsc-generate_solvate.inp  >  1fsc_min.out
gives output files:

Build, minimize, solvate:

% charmm pdbfile=1fsc solvate=true crystal=true shape=octahedral \
         < fsc-generate_solvate.inp  >  1fsc_solvate_octa.out
gives output files: