3. Usage

Running the program without parameters, the list of the implemented options is shown:

 

VEGA 3.1.0 - (c) 1996-2017, Alessandro Pedretti & Giulio Vistoli
Virtual logP by Bernard Testa et al.
Windows x86 (32 bit) Pentium OpenCL version.

Synopsis: vega INPUT ... -o[OUT.PACK] -f[OUTPUT_FORMAT] -p[FORCE_FIELD]
          -s[POINTS] -g[RADIUS] -c[TEMPLATE] -k[KEYWORDS] -a[RES_NUM]
          -d[DIELECTRIC] -e[MOLNUM] -i[SHELL RAD SHAPE]-j[TORSIONS]
          -l[MOLTYPE] -m[KEYWORDS] -q[METHOD] -r[MODE] -t[SECSTRUCT]
          -v[CPUS] -x[MODE ID] -bhnuwy

a -> renumber residues starting from RES_NUM
b -> don't save the connectivity
c -> charge template
d -> dielectric constant for energy calculation
e -> molecule number for score calculation (0 = last)
f -> output format
g -> probe radius for SAS
h -> show this help
i -> solvate the molecule
j -> define the torsions (ALL, AUTODOCK, FLEX)
k -> keywords for InfoXML and MopInt
l -> add hydrogens (GEN, GENBO, NA, NABO, PROT, PROTBO)
m -> keywords for trajectory analysis
n -> normalize coordinates
o -> output file name
p -> define force field to apply
q -> fix the bond order (ALL, RINGS)
r -> remove hydrogens (ALL, APOLAR)
s -> point density for SAS
t -> change the protein secondary structure
u -> add the side chains to a protein
v -> number of CPUs (0 = all)
w -> remove waters
x -> extract the molecule from the database (NAME name; NUM number)
y -> find the molecules in the assembly

INPUT formats:
 Alchemy, AMMP, Arc, AutoDock 4 DLG, BioDock, CAR, CHARMM CRD, CIF, CML,
 CML 2.0, CPMD XYZ, CRT, CHARMM DCD, Chem3D, ChemDraw CDX, ChemSol, CSSR,

 ESCHER NG, Fasta, GAMESS, Gaussian In/Out, GRAMM, Gromacs/Gromos mol,

 Gromacs TRR, Gromacs XTC, HIN, IFF, InChI, LiGen pocket, MDL, MDL V3000,

 Mol2, Mopac cartesian, Mopac Gaussian Z-matrix, Mopac internal, MSF, NAMD

 binary, PDB, PDBA, PDBF, PDBL, PDBQT, PQR, PQRXML, PSFX, QMC, Quanta CSR,

 RIFF, SDF, TINKER XYZ, XYZ, ZIP.

OUTput formats:
 Calc:       Info, InfoXML, Score.
 Map:        BiosymSrf, ComfaFld, CsvIlm, CsvLogP, CsvMep, CsvSrf,
             QuantaIlm, QuantaLogP, QuantaMep, QuantaSrf.
 Molecule:   Alchemy, AMMP, Biosym, ChemSol, CIF, CML, CML2, CPMDXYZ, CRD,
             CRT, CSSR, Fasta, GAMESS, GaussIn, Gromos, GromosNm, IFF,
             InChI, InChIAux, InChIKey, Indigo, MdlMol, MdlMol3, mmCIF,

             Mol2, MopCar, MopInt, MSF, NamdBin, OldBiosym, PDB, PDB2,

             PDBQ, PDBA, PDBF, PDBL, PDBNOTSTD, PDBQT, PQR, PQRXML,
             PSFX, QMC, RIFF, SMILES, SpilloRBS, VINA, XYZ.
 Plot:       BinPlt, CSV, QuantaPlt.
 Trajectory: TrjDCD, TrjIFF, TrjMol2, TrjPDB, TrjTrr, TrjXtc.
 VRML:       Vrml, VrmlPts, VrmlCpk, VrmlSol.

PACKer formats:
 bz2 (BZip2), gz (GZip), pp (PowerPacker), z (Z-Compress).

Score functions (-f Score -k):
 Broto, Broto2, Broto3, Charmm, Charmm22, Charmm36, CVFF, Elect, ElectDD.

TRAJECTORY keywords (-m):
 Angle A1 A2 A3, Dipole, Distance A1 A2, Extract F1 [F2], GyrRad, ILM,
 LipoleBr, LipoleCr, Ovality, PlaneAng A1 A2 A3 A4 A5 A6, PSA, RMSD,
 Surface A1 ..., SurfDia A1 ..., Torsion A1 A2 A3 A4, VlogP, VolDia,
 Volume.

Secondary structure keywords (-t):
 AlphaHelix, LeftHelix, 310Helix, PiHelix, Beta, BetaAnti, BetaPar.
 or
 TOR=VALUE TOR=VALUE ...
 where TOR is the torsion name (Phi, Psi, Omega) and VALUE is the
 torsion value in degree.

 

All parameters are optional with the exception of the input file name (INPUT).

 

3.1 INPUT ...

This option allows to specify the input file names. VEGA recognizes automatically the format of input files and  the list of supported input formats is shown running VEGA without arguments.
You can load more than one file at once with the same or different file formats to create molecular assemblies. The calculation of connectivity is performed separately for each file to prevent connectivity errors when the molecules are overlapped.
The Data Decompressor Engine allows to manage compressed files as normal unpacked files without any external data decompressor. VEGA supports the following compression formats:

Format name File extension
BZip2 .bz2
GZip .gz
PowerPacker .pp
Unix Un/compress .Z

VEGA can recognize .url files and open URLs specified as file names, downloading the molecules for you.

 

3.2 -a[RESNUM]

This option renumbers all residues starting from [RES_NUM]. If this value is not specified, VEGA starts from one. The residue renumbering is very useful when you create an assembly starting from two or more molecules.

 

3.3 -b

This switch saves molecules without connectivity records when the output format can store this kind of information (e.g. PDB, PDBF, IFF). Many molecular packages interpret incorrectly the CONECT field in PDB files, therefore, to solve this problem, you can save the molecule without connectivity.

 

3.4 -c[TEMPLATE]

Currently, VEGA supports only the Gasteiger-Marsili method (gasteiger template). This approach uses a multi-step procedure:

 

3.5 -d[DIELECTRIC]

Use this option If you want to calculate the interaction energy (see -f[FORMAT] option) changing  the default dielectric constant (1.0). Please note that the default value of dielectric constant is stored in the prefs file.

 

3.6 -e[MOLNUM]

This is a compulsory parameter for the interaction energy evaluation (docking score evaluation, see -f[FORMAT] option). It is required to know which molecule (ligand) is considered to evaluate the interaction energy. You can specify 0 as molecule number to indicate the last molecule in the assembly.

 

WARNING:
the IFF/RIFF file format is the only one that is able to contain the molecule number information. For this reason, it's impossible to select the ligand by molecule number if you use assemblies (files containing more than one molecule) in other formats. To skip the problem, you can build the assembly on-the-fly specifying the ligand and the receptor as in the following example:

vega receptor.pdb ligand.pdb -f score -c gasteiger -k "CHARMM36 ELECT" -e 0 -o receptor-ligand.xml

Another solution is the use of -y options that enables the detection of molecules:

vega assembly.pdb -f score -c gasteiger -k BRORO -e 2 -o score.xml -y

 

3.7 -f[OUT.PACK]

With this parameter, you can create an output file in a specific file format. If -f is omitted, the default output format is PDB full standard (see PDB specifications) unpacked. OUT indicates the format and PACK is the optional compression method (bz2, gz, pp and z, see INPUT). This two keywords are case-insensitive.

e.g.    -f CSSR    CSSR output without compression.
-f pdb.Z PDB output with Unix compression.
-f xyz.bz2 XYZ  output with BZip2 compression.

 

3.7.1 Calculation formats

Keyword Description

INFO

Information about the molecule.

INFOXML Same of above but the results are included in a XML file.
Score Evaluation of interaction energy (molecular docking score).

 

3.7.1.1 Information about the molecule

If you want more information about the input molecule, you can use -f INFO option. When you select this operation, VEGA shows many information: total number of atoms, number of heavy atoms, number of residues, number of molecules contained, number of water molecules, molecular weight, coordinates of geometric center, coordinates of mass center, approximative dimensions, total charge (calculated using the atomic charges), dipole, surface area, surface diameter, volume, volume diameter, ovality (only if the probe radius used for surface calculation is null, see -g option), Crippen's logP and lipole, Broto's logP and lipole, Virtual logP (available only in full release), predicted charge (only for proteins, it's calculated searching ionizable groups), aminoacidic charge (only for proteins, it's calculated at physiological pH on the basis of aminoacidic composition), aminoacidic or nucleotidic composition:

************************************
**** Information about molecule ****
************************************

Atoms..............: 48
Heavy atoms........: 25
Residues...........: 1
Molecules..........: 1
Waters.............: 0
Formula............: C19H23NO5
Molecular weight...: 345.384 Daltons
Monoisotopic mass..: 345.157623 Daltons
Geometry center....: 7.1076 3.6789 0.5790
Mass center........: 6.9492 3.5914 0.5256
Appx. dimensions...: 17.4088 10.7721 10.7163
Total charge.......: 0.0003
Dipole.............: 1.0292 Debye
Surf. area (0.00)..: 383.3 Ų (ds=11.0 )
Polar area (PSA)...: 50.6 Ų (apolar=332.7 Ų)
Volume.............: 362.3 ų (dv=8.8 )
Ovality............: 1.6
logP (Crippen).....: 1.9275
Lipole (Crippen)...: 0.4363
logP (Broto).......: 3.0390
Lipole (Broto).....: 0.4755
Virtual logP.......: 3.1402

Please note that the total number of atoms exceeds the MAXATMINFO key in prefs file, surface area, surface diameter, volume, volume diameter, ovality and logP values are not shown.
If the molecule is a protein or a nucleic acid, the following data are shown:

...
Total charge.......: -23.0004
Predicted charge...: -24
Aminoacidic charge.: -24 
Aminoacidic composition:
Res    N.   N. %     Mass     Mass %
====================================
ALA    46   6.29  3269.690    3.57
ARG    42   5.75  6618.506    7.22
ASN    29   3.97  3309.140    3.61
ASP    43   5.88  4921.520    5.37
CYS    18   2.46  1855.515    2.02
GLU    53   7.25  6789.680    7.41
GLN    46   6.29  5894.132    6.43
GLY    40   5.47  2282.165    2.49
HIS    26   3.56  3565.805    3.89
ILE    37   5.06  4186.861    4.57
LEU    86  11.76  9731.422   10.62
LYS    30   4.10  3875.539    4.23
MET    11   1.50  1443.115    1.57
PHE    25   3.42  3681.328    4.02
PRO    35   4.79  3401.088    3.71
SER    42   5.75  3657.370    3.99
THR    24   3.28  2426.550    2.65
TRP    17   2.33  3165.578    3.45
TYR    35   4.79  5710.992    6.23
VAL    46   6.29  4560.075    4.98

WARNING:
If the protein doesn't have got hydrogens, the predicted charge isn't shown. If protein contains special non-aminoacidic groups and/or metal ions, the predicted charge can be incorrect.

 

3.7.1.2 Evaluation of interaction energy (molecular docking score)

VEGA can evaluate the ligand-biomacromolecule interaction energy through molecular mechanics calculations. Some scoring functions are implemented (for more details, see -k option).At the present time, only the CVFF force field is implemented. Please remember that ligand and receptor must have correctly assigned charges  (see  -c option) if you want to calculate the electrostatic interaction. You can specify the dielectric constant with -d option (default 1.0) and the ligand (see -e option). After the energy calculation, VEGA shows (or writes in a XML file) the total interaction energy, the components for each atom and residue.

 

3.7.2 Molecule formats

Keyword Description
ALCHEMY Alchemy format.
AMMP AMMP molecular mechanics software.

BIOSYM

New Biosym .car file (archive 3).

ChemSol ChemSol 2 solvatation energy software.
CIF IUCr Crystallographic Information Framework.
CML Chemical Markup Language (CML) version 1.0.
CML2 Chemical Markup Language (CML) version 2.0.

CRD

CHARMM text file format.

CRT

Indiana University Molecular Structure Center (IUMSC) CRT format for crystallographic structures.

CPMDXYZ CPMD (Car-Parrinello Molecular Dynamics Code) Cartesian output file.

CSSR

Cambridge Data File.

FASTA

FASTA is not a real molecular file, because it can store only the primary structure of proteins and DNA/RNA sequences.

GAMESS Cartesian GAMESS format.
GAUSSIN Gaussian Cartesian input.

GROMOS

This is the special file format of the molecular mechanics package Gromos/Gromacs.

GROMOSNM

GROMOS with the coordinates in nanometers.

IFF

Interchange File Format. This is a binary file with an AmigaOS chunk structure (like IFF-ILBM, AIFF, etc). All chunks are optional and the structure is totally expandable (see Appendix D).

INCHI IUPAC Chemical Identifier (InChI).
INCHIAUX Same of above with auxiliary data.
INFOXML

This is not a real file molecule file format, because it's a XML container of property data only. The user can select the properties to calculate including the -k[KEYWORDS] option.

MDLMOL MDL Molfile.
MMCIF Crystallographic Information Framework for macromolecules.

MOL2

Tripos Sybyl Mol2 file format.

MOPCAR Mopac cartesian coordinate file (see below).

MOPINT

The Mopac internal coordinates file (.dat) is useful to link Mopac with other software packages. The Mopac keyword CHARGE is automatically calculated by atomic charges. Other keywords can be specified with -k[KEYWORDS] option. The preferences file of VEGA (prefs in Data directory) contains a special record Mopac keyword used by default.

MSF

MSI Quanta binary file. Its complexity and the poor documentation available have not allowed a full implementation of this format. You can only overwrite an existing MSF file (that must be compatible with the input), but not create a new file.

NAMDBIN NAMD .coor double precision binary coordinate file.

OLDBIOSYM

Old Biosym (Accelrys) .car file (archive 1).

PDB PDB pre-2.0 specifications.

PDB2

PDB 2.2 full standard (default).

PDBA

PDB full standard with special records to include atomic charges, force field parameters and ATDL description for each atom.   It's totally compatible with the PDB standard, because the extra information are placed in REMARK records.

PDBF

PDB full standard with special REMARK records to include atomic charges and force field parameters. It's also totally compatible with the PDB standard.

PDBL

The PDB Large file format allows to save molecules with more than 99999 atoms, inserting a TER record after 99999 atoms and restarting the numbering from 1. It's full compatible with the NAMD package and doesn't support the connectivity (CONECT record).

PDBNOTSTD

Simplified PDB format, more compatible with software packages that have a partial implementation of Brookhaven specifications. Special records (HETATM, TER, CONECT and MASTER) are not used.

PDBQ

PDB full standard with atomic charges placed in the last right column.

PDBQT

AutoDock 4 PDBQT. It's a standard PDB file with two extra columns for charges and potentials. It could contains the information for the torsion angles.

PQR

Modified PDB file with atomic charges and Van der Waals radii in the Occupancy and TempFactor columns. It's the format required by APBS.

PQRXML XML-based format used by APBS.
PSFX PSF topology in X-Plor sub-format required for molecular dynamics (e.g. CHARMM and NAMD).
QMC CSSR variant.
RIFF Interchange File Format (IFF) variant in little endian format  (see Appendix D).
SMILES Simplified molecular input line entry specification (SMILES canonical format).
SPILLORBS Spillo Reference Binding Site.
VINA AutoDock Vina PDBQT. It's a standard PDB file with two extra columns for charges and potentials. It could contains the information for the torsion angles.

XYZ

Cartesian coordinates file. The first record is the total number of atoms and the next records are for each atom. The atom record contains the element name and X, Y, Z Cartesian coordinates.

 

3.7.3 Plot formats

All these output formats are useful for trajectory analysis (see -m [KEYWORDS] option)

Keyword Description

BINPLT

Generic binary plot. It's a sequence of single precision floats in big endian format.

CSV

ASCII text file with each field separated by a semicolon.

QUANTAPLT

Accelrys Quanta plot file.

 

3.7.4 Surface and map formats

VEGA can calculate Van Der Waals and accessible to solvent molecular surface. To enable this function, you have to use the -f[OUTPUT_FORMAT] option as shown in the following table:

Keyword Type Description
COMFAFLD Text COMFA 3D field. When you select this output, you must specify the field type with -m[KEYWORD] option. A Sybyl .rgn file is needed as input also. At the present time, the only implemented filed is vlogP*.

BIOSYMSRF

Text

Van Der Waals and accessible to solvent molecular surface for Insight II package.

CSVILM Text Molecular hydropathicity index (ILM) surface in CSV (Comma Separated Values) format.

CSVLOGP*

Text

Virtual logP surface in CSV format.

CSVMEP

Text

Molecular Electronic Potential (MEP) in CSV format.

CSVSRF

Text

Van Der Waals and accessible to solvent molecular surface in CSV format.

QUANTAILM Binary Molecular hydropathicity index (ILM) surface in Quanta format.

QUANTALOGP

Binary

Virtual logP surface in Quanta format.

QUANTAMEP

Binary

Molecular Electronic Potential (MEP) in Quanta format.

QUANTASRF

Binary

Van Der Waals and accessible to solvent molecular surface for Quanta package.

The default calculation is the water accessible surface  (1.4 sphere radius). To change the solvent radius (probe), you can use the -g[RADIUS] option. If you set the probe radius to null, VEGA calculates the Van Der Waals surface. The standard point density is 10 for one 2. See -s[POINTS] option to change this value. Click here if you want more information about the surface calculation method.

 

3.7.5 VRML formats

In order to support the Web publishing, the Virtual Reality Modeling Language (VRML) was implemented in VEGA. To use this function you can use the -f[OUTPUT_FORMAT] option with the following keywords:

Keyword VRML output

VRML

VRML 1.0 wireframe representation with standard coloring method.

VRMLCPK

VRML 1.0 CPK representation with standard coloring method.

VRMLPTS

VRML 1.0 dotted surface representation.

VRMLSOL

VRML 1.0 Van Der Waals and accessible to solvent molecular solid surface

The VRML surface formats can also accept the same options of standard surface outputs (see section 3.7.4).

 

3.7.6 Trajectory formats

VEGA can convert the trajectory files of molecular dynamics simulations to different formats. To enable this function, you have to use the -f[OUTPUT_FORMAT] option as shown in the following table:

 

Keyword Type Compression Description
TRJDCD Binary No CHARMM/NAMD DCD binary file.
TRJIFF Binary No IFF/RIFF 64 bit binary file.
TRJMOL2 Text No Mol2 multi model.
TRJPDB Text No PDB multi model.
TRJTRR Binary No Gromacs TRR.
TRJXTC Binary Yes Gromacs XTC (lossy compression).

 

3.8 -g[RADIUS]

If you want calculate a surface map with a probe radius different than the default one (the default value is the 1.4 water radius) without change the prefs file, you can use this option. Please remember that in orded to calculate the Van Der Waals surface, you must set this parameter to zero.

 

3.9 -i[SHELL RAD SHAPE]

VEGA can solvate a molecule virtually with any type of solvent (e.g. H2O, CCl4, etc). The cluster file must be placed in Data/Clusters (Data\Clusters) directory and can be in any VEGA supported format (also packed). This is a solvent assembly with cubic shape (usually with dimension of 50x50x50 ), optimized, with uppercase file name without extension (e.g. WATER, CCL4, etc).
SHELL is the solvent cluster name (e.g. WATER). SHAPE is the form of solvatation cluster: BOX for cubic clusters, SPHERE for spherical clusters and LAYER to solvate with a layer of solvent. RAD is a value in that followed by BOX, defines the box side, by SPHERE, the sphere radius and by LAYER the layer thickness.

 

3.10 -j[TORSIONS]

This option define the torsion angles in the molecule. It can be used with the file formats that require the torsions (e.g. AutoDock's PDBQT).

Argument Description
ALL Define all possible torsions.
AUTODOCK Define the flexible torsions for AutoDock 4.
FLEX Define the flexible torsions only.

 

3.11 -k[KEYWORDS]

This option is useful to pass the control keywords when the Info XML (-f NFOXML option) or the Mopac  (-f MOPINT option) or the Score  (-f Score option) format is selected. Remember to use quotas (") if the number of keyword is more than one. In the prefs file, you can specify the default Mopac keywords. The Info XML keywords are summarized in the following table:

Keyword Calculated property
ALL All properties (default option).
AREA Surface area and surface diameter.
ATOMS Number of atoms.
ATMTYPES Atom types.
CENTGEO Geometric center.
CENTMASS Center of mass.
CENTROIDS Number of centroids.
CHAINS Number of chains
CHARGE Total charge.
CHIRALATMS List of the chiral atoms.
CHIRALNUM Number of the chiral atoms.
DIMENSIONS Molecule dimensions.
DIPOLE Dipole moment.
EZBONDS List of the bonds with E/Z geometry.
EZNUM Number of the bonds with E/Z geometry.
FORMULA Molecular formula.
GCMR Molar refractivity (Ghose & Crippen method).
GYRRAD Radius of gyration.
HBONDACC Number of H-bond acceptors (N and O only).
HBONDDON Number of H-bond donors (H-N and H-O only).
HEAVYATOMS Number of heavy atoms.
HLB Davies, Griffin, PSA-based and mean hydrophilic-lipophilic balances (HLBs).
HYDROGENS Number of hydrogens.
ISOTOPIC Isotopic distribution (isotopic pattern). Format: mass probability (%)
LOGPCRIPPEN Ghoose & Crippen logP and lipole.
LOGPBROTO Broto & Moreau logP and lipole.
LOGPVIRTUAL Bernard Testa's virtual logP.
MIMASS Monoisotopic mass.
MOLECULES Number of molecules.
MOLNAME Molecule name.
PROBERAD Probe radius used in the surface calculation (AREA).
PSA Polar and apolar surface areas.
RESIDUES Number of residues.
SEGMENTS Number of segments.
SMILES SMILES string.
TORADOCKNUM

Number of flexible torsions used by AutoDock to perform the in situ conformational search.

TORFLEXNUM Number of flexible torsions.
TORNUM Number of torsions.
VOLUME Molecular volume and volume diameter.
WATERS Number of waters.
WEIGHT Molecular weight.

All these keywords can be combined separating them by a space character.

The Score keywords that can be used to select one or more score functions, are summarized in the following table:

Keyword Score function
CHARMM R6-R12 non-bond interaction evaluated by CHARMM 22 force field provided by Accelrys. To perform this calculation, the parm.prm file must be copied in the ...\VEGA\Data\Parameters directory. This file is not included in the package for copyright reasons.
CHARMM22 R6-R12 non-bond interaction evaluated by CHARMM 22 force field.
CHARMM36 R6-R12 non-bond interaction evaluated by CHARMM 36 force field.
CVFF R6-R12 non-bond interaction evaluated by CVFF force field.
ELECT Electrostatic interaction. To change the dielectric constant value, use the -d option.
ELECTDD Distance-dependent electrostatic interaction. To change the dielectric constant value, use the -d option.
MLPINS Hydrophobic interaction calculated using the Broto's and Moreau's atomic constants*.
MLPINS2 Hydrophobic interaction in which the distance between interacting atom pairs is considered as square value*.
MLPINS3 Hydrophobic interaction in which the distance between interacting atom pairs is considered as cube value*.
MLPINSF Hydrophobic interaction in which the distance is evaluated by the Fermi's equation*.

All these keywords can be combined separating them by a space character also.

 

* From Vitoli G. et al., Bioorg. Med. Chem. 18 (2010) 320-19.

 

"The MLP Interaction Score (MLPInS) is computed using the atomic fragmental system proposed by Broto and Moreau and a distance function that define how the score decrease with increasing distance between interacting atoms. In detail, the equation to compute such an interaction score is reported below:

 

MLPInS equation

 

where fa and fb denote the lipophilicity increments for a pair of atoms and rab  is the distance between them. The first sum (p) concerns all ligand’s atoms and the second (m) all enzyme’s atoms. The basic assumption in the calculation of the MLPInS, which encodes the contributions of the various intermolecular forces measured experimentally in partition coefficients, is that the score is favourable (i.e. negative) when both increments have the same sign (as denoted by the negative sign in in the equation), or unfavorable (repulsive forces) when the score has a positive sign. When the atomic parameters are both positive, MLPInS encodes hydrophobic interactions and dispersion forces, the importance of which is well recognized in docking simulations, and it accounts for polar interactions, in particular H-bonds and electrostatic forces when the atom ic parameters are both negative".

 

3.12 -l[MOLTYPE]

This command adds the hydrogens to the loaded molecule/s, saturating all atom valences. MOLTYPE is the molecule type and it can be:

MolType Description
GEN Generic organic molecule.
GENBO Generic organic molecule, bond order algorithm.
NA Nucleic acid.
NABO Nucleic acid, bond order algorithm.
PROT Protein.
PROTBO Protein, bond order algorithm.

Use the bond order algorithm if the molecule geometry is uncertain (e.g. raw 3D structure or 2D structure), but it works well only if the bond order is correctly assigned.

 

3.13 -m[KEYWORDS]

This option allows to do measures for each frame or to extract one or more frames of a molecular dynamics trajectory file. You must specify a keyword to set  the kind of measure and optionally  the atom selection:

Keyword Description
ANGLE A1 A2 A3 Bond angle.
DISTANCE A1 A2 Bond length.
DIPOLE Molecular dipolar moment.
EXTRACT F1 [F2]

Extract one ore more molecules from the trajectory file starting from the F1 frame to the F2 frame. F2 is optional and if it's omitted, the extraction proceed until the last frame.

GYRRAD Gyration radius.
ILM Molecular hydropathicity index (water cluster required).
LIPOLEBR Lipole (Broto & Moreau)
LIPOLECR Lipole (Ghoose & Crippen)
SURFACE A1 ... Surface area.
SURFDIA A1 ... Surface diameter. It's the diameter of a theoretical sphere
with the surface area of the molecule.
OVALITY Ovality. It's calculated by the following equation:

Ovality equation

where:

O = ovality;

A = area;

V = volume

PLANEANG A1 A2 A3 A4 A5 A6 Angle between planes defined by A1, A2, A3 and A4, A5, A6.
PSA Polar surface area.
RMSD Superimpose two subsequent frames and calculate their RMS (Root Mean Square). This operation is called RMSD.
TORSION A1 A2 A3 A4 Torsion angle.
VLOGP Virtual logP.
VOLUME Molecular volume.
VOLDIA Volume diameter.  It's the diameter of a theoretical sphere
with the volume of the molecule.

To select each atom required in the mesure (e.g. A1 A2 etc), you must use  the atom number only, or the following syntax: ATOM:RESNAME:RESNUM. RESNAME and RESNUM are optional if ATOM is univocal. Suppose to have a benzene ring and you would like indicate the third atom, like shown in the following PDB file:

...
ATOM      2  C2  BEN     1       -0.695   1.203  -0.002  1.00  0.00
ATOM      3  C3  BEN     1       -1.389   0.000  -0.006  1.00  0.00
ATOM      4  C4  BEN     1       -0.695  -1.203  -0.007  1.00  0.00
...

you can use, without differences, 3 or C3 or C3:BEN or C3:BEN:1. If you want select the atom 482 in a polypeptidic sequence where only one proline is present, you can indicate it with 482 or CA:PRO or CA:PRO:32, but not CA only:

...
ATOM    481  N   PRO    32      -29.658  -2.153   7.524  1.00  0.00
ATOM    482  CA  PRO    32      -28.294  -1.798   7.139  1.00  0.00
ATOM    483  C   PRO    32      -27.169  -2.471   7.908  1.00  0.00
...
ATOM    495  N   VAL    33      -25.978  -2.393   7.325  1.00  0.00
ATOM    496  CA  VAL    33      -24.749  -2.884   7.927  1.00  0.00
ATOM    497  C   VAL    33      -23.841  -1.699   7.661  1.00  0.00
...

 

If more than one proline is present in this sequence, you can't use CA:PRO neither.

At the end of the property calculation, VEGA shows the ranges, the average value and the standard deviation. If you want exclude the influence of the water in the calculation of dipolar moment, molecular surface, Virtual logP and molecular volume, you can use the -w option.

 

3.14 -n

This switch enables the normalization of atomic coordinates. The geometry center of a single molecule or a complex is moved to the origin of Cartesian axes.

 

3.15 -o[OUTPUT]

With -o parameter, you can specify the name of the output file with or without extension. If the filename doesn't have any extension, VEGA automatically adds the appropriate one on the basis of the selected output format (see -f option). The most common extension used by VEGA are shown in the following table:

Extension Type Add File format
.alc T Y Alchemy.
.amp T Y AMMP.

.arc

T

N

Mopac optimized internal coordinates.

.car

T

Y

Accelrys CAR file (old and new subformat).

.cif T Y IUCr Crystallographic Information Framework (CIF/mmCIF).
.cml

T

Y

Chemical Markup Language (CML).

.cor

T

Y

Accelrys CAR file with optimized coordinates.

.crd

T

Y

CHARMM.

.crt T A IUMSC CRT.
.cs T Y ChemSol 2.

.cssr

T

Y

Cambridge Data File (CSSR).

.csv T Y Surface in CSV format.

.dat

T

Y

Mopac cartesian/internal coordinates.

.dcd

B

Y

CHARMM/NAMD trajectory file.

.ene

T

N

Accelrys CHARMm energy file.

.ene

T

Y

VEGA interaction energy file.

.ent

T

N

PDB.

.fas

T

Y

FASTA.

.fld T Y Tripos COMFA field.

.gro

T

Y

Gromos/Gromacs.

.iff

B

Y

Interchange File Format (IFF).

.inc T N InChI.
.inchi T Y InChI.

.inf

T

Y

VEGA information file.

.inp T Y GAMESS cartesian.
.log T Y Gaussian output.

.ml2

T

Y

Tripos Sybyl Mol 2.

.mol T Y MDL Molfile (V2000), MDL Extended Molfile (V3000).

.msf

B

Y

MSI Quanta.

.par

T

N

VEGA parameters.

.pdb

T

Y

PDB, PDB2, PDBA, PDBF, PDBL and PDBQ.

.pdbqt T Y AutoDock 4 / Vina PDBQT.
.pqr

T

T

PQR.
.psf T Y PSF and PSF X-Plor.

.qmc

T

N

QMC (CSSR like format).

.smi

T

Y

Smiles.

.srf

B

Y

Accelrys Quanta surface.

.srf

T

Y

Accelrys  Insight surface.

.tem

T

N

VEGA template.

.wrl

T

Y

VRML (Virtual Reality Markup Language).

.xml

T

Y

PQR XML.
.xyz T Y CPMD XYZ.
.xyz T Y TINKER XYZ.

.xyz

T

Y

XYZ.

Where the column Extension is the file extension, Type is the file type (T = text, B = binary), Add shows if VEGA adds automatically the extension and File Format is the name of file format.
If you execute VEGA without -o parameter, the output is redirected to the console (stdout) or to a special device driver (e.g. PRT: for AmigaDOS). This function is very useful to interface VEGA with another program that can get the input from console. The redirection is possible with text file formats only.

 

3.16 -p[FORCE_FIELD]

This function allows to assign the atom types using a specified force field template. This is the most complex function implemented in VEGA. The first challenge being the creation of an universal language, called ATDL (Atom Type Description Language) able to describe virtually any atom type. For more information about ATDL, click here. VEGA uses the force field template files stored in Data directory with the extension .tem (lowercase). The name of these files must be uppercase, but the argument of -p option is case-insensitive. In order to assign the correct atom types, VEGA uses a multiple step algorithm:

Although these steps are very complex, the total process speed is very high.

 

3.17 -q[METHOD]

Fix the bond order using the specified method that could be: ALL (find the order of all bond) or RINGS (fix the bonds of the aromatic rings making them partial double).

 

3.18 -r[MODE]

This switch removes the hydrogen atoms: the empty or ALL arguments remove all hydrogens and the APOLAR removes the apolar hydrogens only.

 

3.19 -s[POINTS]

With this parameter you can change the point density of a surface map. POINTS is the number of points per surface unit (2). The default value is stored in the prefs file and usually it is set to 10. For more information about surface calculation, please see the -f[FORMAT] option.

 

3.20 -t[SECSTRUCT]

The -t option allows to change the protein secondary structure. Two operational mode are available: in the former the user assigns Phi, Psi and Omega torsion values by the syntax TORSION_NAME=value (e.g. Phi=-135), in the latter he put secondary structure name as reported in the following table:

Sec. structure name Phi Psi Omega Description
AlphaHelix -57.8 -47.0 180.0 Alpha helix (3,6.13).
LeftHelix 57.8 47.0 180.0 Left handed alpha helix.
310Helix -74.0 -4.0 180.0 3.10 helix.
PiHelix -57.1 -69.7 180.0 Pi helix
Beta -135.0 135.0 180.0 Generic beta strand.
BetaAnti -140.0 135.0 180.0 Beta strand in anti-parallel sheet.
BetaPar -120.0 115.0 180.0 Beta strand in parallel sheet.

This option can be used to assign the secondary structure when a Fasta file is loading and if it's omitted, the generic beta strand structure is assigned. All sub-parameters are case insensitive.

 

3.21 -u

This command adds the side chains to a protein. The side chain database is placed in the Data/Fragments directory and it's called Amino acids L.zip. The side chains are added without hydrogens and so, if you need them, you must use the -l option also.

 

3.22 -v[CPUS]

Set the number of CPUs used in the parallel calculations. The 0 argument means that all installed CPUs are used.

 

3.23 -w

This switch removes all the water molecules present in an assembly. Please note that VEGA do not find the water molecules by residue names (e.g. HOH, TIP3, etc), but on the basis of connectivity table. This approach is slower but more precise and independent of residue naming.
You can use the -w option in trajectory analysis to neglect the water influence in the evaluation of dipolar moment, molecular surface and Virtual logP.

 

3.24 -x[MODE ID]

It extracts a molecule from the input database that must be in SDF or ZIP format. The arguments of this  options can be:

Argument 1 Argument 2 Description
NAME molecule name Extract the molecule with the specified name.
NUM molecule number Extract the molecule with the specified identification number.

 

3.25 -y

Find the molecules in the assembly using the connectivity information. This feature is useful when you need to select the molecule (ligand) in the interaction energy evaluation (see -e and -k options), because all file formats, excluding IFF/RIFF, can't store molecule information (starting and ending atoms) in the atom list.