4. Examples
- vega
lists the available options.
- vega my_file.car
reads my_file.car in Biosym format and shows the
converted file in PDB format with connectivity.
- vega my_file.cssr f info
reads my_file.cssr in CSSR format and shows its properties.
- vega my_file.car o new_file b -n
reads my_file.car, normalizes the coordinates and writes new_file.pdb in PDB
format without connectivity, adding .pdb to output file name.
- vega my_file.arc o new_file.car f biosym p cvff
reads my_file.arc in Mopac format, assigns atom types, writes new_file.car in new
Biosym format keeping Mopac charges.
- vega file1.pdb file2.dat o assembly f iff -w -a
reads file1.pdb and file2.dat creating an assembly, removes all water
molecules, renumbers the residues and writes assembly.iff in Interchange File
Format.
- vega my_file.mol2 o new_file p cvff c gasteiger f pdbf
translates my_file.mol2 from Tripos Mol2 to PDB Fat format creating new_file.pdb.
Atom types are assigned using the CVFF force field and the atomic charges using the
Gasteiger method.
- vega receptor.car ligand.car f cvff d 30 e 9999
calculates the interaction energy between receptor.car and ligand.car with
CVFF force field parameters, 30 for dielectric constant and shows the results in console.
9999 is the residue number of ligand.
- vega my_file.msf o surface.srf f QuantaSrf s 20
calculates the surface accessible to solvent using the default probe radius and 20 for
point density and saves it in the binary file surface.srf compatible with Quanta
package.
- vega my_file.msf o surface f BiosymSrf g 0
calculates the Van Der Waals surface using default point density and saves it in the ASCII
file surface.srf compatible with Insight II package.