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The scripts.tar.gz tar ball contains following scripts:, along with a small set of auxiliary (data) files. These scripts are also available on this link, and questions about how to use these scripts are addressed in this thread on the CHARMM forums.
| Section |
|---|
| Column |
|---|
| system setup
add-ions.str
gen-alpha-helix.inp
gen-dna.inp
gen-prot.inp
minimize.inp
rename-2pdb.str
setup-truncated-octahedron.str
solvent-box.str
solvent-shell.str
solvent-sphere.str |
| Column |
|---|
| dynamics
dynamics.inp
noe-dynamics.inp
run-cpt-md.inp
run-pbc-md.inp
run-sdb-md.inp |
| Column |
|---|
| analysis
asa-protein.str
extract-coordinate-frame.inp
hbonds.inp
interaction-energy.inp
merge-orient-trajectory.inp
merge-recenter-trajectory.inp
rmsd-nucleotide.str
rmsd-residue.str
rmsd-rgyr.inp
rmsf-nucleotide.str
rmsf-residue.str
self-diffusion-coeff.inp
trp-anisotropy.inp |
|
There is also a small set of auxiliary (data) files.
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VMD TCL script to calculate density profile normal to z-axis
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