4. Command line examples

• vega
  show the available options.

• vega my_file.car
  read my_file.car in Biosym format and print the converted file in PDB format with connectivity.

• vega my_file.cssr.gz -f info
  read my_file.cssr.gz,  uncompress it and show the molecular properties.

• vega "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1QBQ" -o 1QBQ.iff -f iff
  download the molecule from PDB and save it in IFF format.

• vega my_file.car -o new_file -b -n
  read my_file.car, normalize the coordinates and write new_file.pdb in PDB format without connectivity, adding .pdb to the output file name.

• vega my_file.arc -o new_file.car -f biosym -p cvff
  read my_file.arc in Mopac format, assign atom types and write new_file.car in new Biosym format keeping Mopac charges.

• vega file1.pdb file2.dat -o assembly.iff -f iff -w -a
  read file1.pdb and file2.dat creating an assembly, remove all water molecules, renumber the residues and write assembly.iff in Interchange File Format (IFF).

• vega my_file.mol2 -o new_file -p cvff -c gasteiger -f pdbf
  translate my_file.mol2 from Tripos Mol2 to PDB Fat format creating new_file.pdb. The atom types are assigned, using the CVFF force field and the atomic charges, using the Gasteiger method.

• vega receptor.car ligand.car -f score -k "BROTO CHARMM36" -d 30 -e 0
  calculate the BROTO and CHARMM36 interaction energies between receptor.car and ligand.car with 30 for dielectric constant and shows the results in console. 0 indicates the last molecule in the assembly (ligand.car)

• vega my_file.msf -o surface.srf -f QuantaSrf -s 20
  calculate the surface accessible to solvent (SAS) using the default probe radius and 20 as point density and save it in surface.srf binary file compatible with Quanta package.

• vega my_file.msf -o surface -f BiosymSrf -g 0
  calculate the Van Der Waals surface using default point density and save it in surface.srf ASCII file compatible with Insight II package.
  

• vega my_trajectory.CRD -o my_mesure.csv -f csv -m distance CA:ALA:1 360
  analyze a CHARMm trajectory file measuring the distance between two atoms and storing all data in the my_measure.csv file.

• vega my_file.hin -o solvated.pdb -i water 10 sphere
  solvate my_file.hin with a spherical water cluster of 10 Å radius.

• vega my_file.fas -o my_file_3d.iff -f Iff -t AlphaHelix
  load my_file.fas, assign secondary structure as alpha helix and save it in IFF format.

• vega my_file.pdb -o my_file_3d -t phi=-135 psi=135
  load my_file.pdb, change the secondary structure and save it in PDB format, adding the .pdb file extension.

• vega my_file.pdb -o my_file -f PDBQT -c Gasteiger -p AutoDock -r Apolar -j Flex
  load my_file.pdb, assign the Gasteiger-Marsili atom charges, assign the AutoDock atom types, remove the apolar hydrogens, find the flexible torsion angles and save the molecule in PDBQT format.

• vega complex.pdb -o score.xml -f Score -c Gasteiger -e 2 -k "BROTO ELECT" -y
  load assembly.pdb, assign the Gasteiger-Marsili atom charges, find the molecules, calculate the BROTO (hydrophilic interaction) and ELECT (electrostatic interaction) scores, considering as ligand the second molecule in the assembly and finally save the results in XML format.