4. Examples
vega
lists the available options or starts the graphic interface (only for Win32 version).
vega my_file.car
reads my_file.carin Biosym format and shows the
converted file in PDB format with connectivity.
vega my_file.cssr.gz -f info
reads my_file.cssr.gz, uncompress it and shows the molecular
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.iff -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 score -k "BROTO CHARMM36" -d 30 -e 0
calculates 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
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.
vega my_trajectory.CRD -o my_mesure.csv -f csv -m distance
CA:ALA:1 360
analyzes a CHARMm trajectory file measuring the distance between two atoms and storing all
data in a csv file.
vega my_file.hin -o solvated.pdb -i water 10 sphere
solvates my_file with a spherical water cluster of 10 Å radius.
vega my_file.fas -o my_file_3d.iff -f Iff -t AlphaHelix
loads my_file.fas, assigns the alpha helix secondary structure and saves
it in IFF format.
vega my_file.pdb -o my_file_3d -t phi=-135 psi=135
loads my_file.pdb, changes its secondary structure and saves
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
loads my_file.pdb, assigns the Gasteiger-Marsili atom charges,
assigns the AutoDock atom types, removes the apolar hydrogens, finds the
flexible torsion angles and saves the molecule in PDBQT format.
vega complex.pdb -o score.xml -f Score -c Gasteiger -e 2 -k "BROTO
ELECT" -y
loads assembly.pdb, assigns 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 saves the
results in XML format.