3. Usage

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

VEGA 3.2.3 - (c) 1996-2023, Alessandro Pedretti & Giulio Vistoli
Virtual logP by Bernard Testa et al.
Windows x64 (64 bit) 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)] -z[NTERM CTERM] -0bhnuwy
 

0 -> ignore locale settings of the decimal separator
a -> renumber residues starting from RES_NUM
b -> don't save the connectivity
c -> charge template (FORMAL, GASTEIGER, ...)
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 -> list/extract molecule/s from a database (LIST; NAME name; NUM number)
y -> find the molecules in the assembly
z -> N-term and C-term capping for peptide (default: NONE NONE)

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,

 EMPIRE, 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,
 RMSDH, RMSDALN, RMSDALNH, RMSDSYMCOR, RMSDSYMCORH, 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.

Peptide capping keywords (-z):
 NTERM: NONE, H3N+, HCONH, H3CCONH
 CTERM: NONE, O-, OH, OCH3, OC2H5

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:

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

3.2 -0

With this option, VEGA ignores the locale settings and writes always a dot (.) as decimal separator.

3.3 -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.

3.4 -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.

3.5 -c[TEMPLATE]

Currently, VEGA supports formal charges (formal keyword), atomic charges based on a fragment database (charmm22_char, charmm36_char, opls_char keywords) and atomic charges based on the Gasteiger-Marsili method (gasteiger keyword) . The Gasteiger-Marsili approach is based on a multi-step procedure:

• Attribution of atom types (by UNIV template).
• Search for explicit charges (e.g. -COO^-, -NH₃⁺, etc).
• Attribution of partial charges through a template (see Appendix A).
• Smoothing of charges.

The formal charges are correctly assigned only if all bonds have the right order (single, double and triple).

3.6 -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.

3.7 -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

3.8 -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.

3.8.1 Calculation formats

3.8.1.1 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 Å)
Polar area (PSA)...: 50.6 Ų (apolar=332.7 Ų)
Volume.............: 362.3 ų (dv=8.8 Å)
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.

3.8.1.2 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.

3.8.2 Molecule formats

3.8.3 Plot formats

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

3.8.4 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:

The default calculation is the water accessible surface  (1.4 Å 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 Ų. See -s[POINTS] option to change this value. Click here if you want more information about the surface calculation method.

3.8.5 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:

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

3.8.6 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:

3.9 -g[RADIUS]

If you want calculate a surface map with a probe radius different than the default one (the default value is the 1.4Å 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.

3.10 -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 Å ), 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 Å that followed by BOX, defines the box side, by SPHERE, the sphere radius and by LAYER the layer thickness.

3.11 -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).

3.12 -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:

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.
CONTACTS	The scores are evaluated by counting the number of ligand/receptor contacts and by normalizing it by the number of heavy atoms and the mass of the ligand. Moreover, if the receptor is a protein, it generates an interaction fingerprint with a size of 20 bits (one bit for each amino acid type) and a contact map in which the number of contacts per amino acid type is reported. To determine if there is a contact between a pair of atoms, the distance between the two centres is calculated and if it is less than 2.5 Å, then there is a contact. This threshold value can be changed in the prefs file. If -o option is used, the resulting XML file will include the also the two additional scores with extra tag (attributes: id = 1 contacts normalized by the number of heavy atoms; id = 2 contacts normalized by mass), the interaction fingerprint  (fingerprint tag) and the contact map (aamap tag).
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 (MLP_InS) 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:

where f_a and f_b denote the lipophilicity increments for a pair of atoms and r_ab  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 MLP_InS, 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, MLP_InS 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".

3.13 -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:

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.

3.14 -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:

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.

3.15 -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.

3.16 -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:

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.

3.17 -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:

• Creation of connectivity table.
• Attribution of hybridization of each atom.
• Search for the rings.
• Search for aromatic systems using the Hückel rule.
• Parsing of the selected ATDL template.
• Final attribution of atom types.

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

3.18 -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).

3.19 -r[MODE]

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

3.20 -s[POINTS]

With this parameter you can change the point density of a surface map. POINTS is the number of points per surface unit (Ų). 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.

3.21 -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:

Through the keyword PATTERN=, you can set the secondary structure for each residue according the previous table (Code column). If you specify U code, Phi, Psi and Omega are retrieved from the user-defined values set as explained above.

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.

3.22 -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.

3.23 -v[CPUS]

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

3.24 -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.

3.25 -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:

3.26 -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.

3.27 -z[NTERM CTERM]

Add the capping to N- and C-term position of a peptide when it is built from its primary sequence while is loaded from a FASTA file.