3. Usage
At the present time, the only way to run VEGA is the execution from a command shell. If you execute the program without parameters, a list of the implemented options is printed:
VEGA V1.1 - (c) 1996-2000, Alessandro
Pedretti & Giulio Vistoli
Virtual logP by Bernard Testa et al.
Windows 9x/NT Pentium version.
Synopsis: vega INPUT ... -o[OUTPUT] -f[OUTPUT_FORMAT] -p[FORCE_FIELD]
-s[POINTS] -g[RADIUS] -c[TEMPLATE]
-k[KEYWORDS] -a[RES_NUM]
-d[DIELECTRIC] -e[NAME:NUM]
-i[SHELL RAD SHAPE] -m[KEYWORDS]
-bnrw
a -> renumber residues starting from RES_NUM
b -> don't save the connectivity
c -> charge template
d -> dielectric constant for energy calculation
e -> residue for energy calculation
f -> output format
g -> probe radius for SAS
h -> show this help
i -> solvate the molecule
k -> keywords for Mopac
n -> normalize coordinates
m -> keywords for trajectory analysis
o -> output file name
p -> define force field to apply
r -> remove hydrogens
s -> point density for SAS
w -> remove waters
INPUT formats:
Biosym, CHARMm CRD, CHARMm DCD, CSSR, Gromos, IFF, Mol2, Mopac, MSF,
PDB, PDBF, QMC, XYZ.
OUTPUT formats:
Calc: CVFF, Info.
Molecule: CRD, CSSR, Fasta, Gromos, GromosNm, IFF, Mol2, MSF, PDB,
PDBQ, PDBF, PDBNOTSTD, QMC,
OldBiosym, Biosym, MopInt,
XYZ.
Plot: BinPlt, CSV, QuantaPlt.
Surface: BiosymSrf, QuantaLogP, QuantaMep, QuantaSrf.
VRML: Vrml, VrmlPts, VrmlCpk, VrmlSol.
TRAJECTORY keywords (-m):
Angle A1 A2 A3, Distance A1 A2, PlaneAng A1 A2 A3 A4 A5 A6, Dipole,
Surface A1 ..., SurfDia A1 ..., Torsion A1 A2 A3 A4, VlogP, Volume,
VolDia.
All parameters are optional with the exception of the input file name (INPUT). The copyright version for logP don't appear if you have a full VEGA release with the logP calculation routines that are not free.
3.1 INPUT
With this option, you can specify the name of the input file. An intelligent algorithm
implemented in VEGA recognizes automatically the input file format. The supported input
formats are: MSI Quanta/CHARMm CRD and DCD, Cambridge Data File (CSSR), Gromos,
Interchange File Format (IFF), Tripos Sybyl (Mol2), MSI Quanta MSF, Protein Data Bank
(PDB), Protein Data Bank Fat (PDBF), MSI/Biosym Insight II (.car), MoPac internal
coordinates, catesian coordinates (XYZ).
You can load more than one file at once with the same or different file formats to create
a molecular assembly. The calculation of connectivity is performed separately for each
file loaded to prevent the connectivity errors of bumping molecules.
3.2 a[RESNUM]
This function 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
With this switch, you can disable the connectivity saving for those molecular formats that
can store such information (e.g. PDB, PDBF, IFF). Many molecular packages interpret
incorrectly the CONECT field in PDB files and thus, to solve this problem, you can save
the molecule without connectivity data.
3.4 c[TEMPLATE]
At the present time, VEGA can assign the partial atomic charges in two ways: the first one
is based on the Gasteiger-Marsili method and the second one relies on a fragment database
with the atomic charges calculated with semiempirical or ab-initio methods. With this
second method you cant assign the charges if the fragment is not present in the
database.
The Gasteiger method is universal and uses a multi-step procedure:
3.5 d[DIELECTRIC]
If you want to calculate the interaction energy (see f[FORMAT]
option) with a specific dielectric constant, you can use this parameter. Please note that
the default value of dielectric constant is stored in the prefs file and usually it
is set to 1.0.
3.6 e[NAME:NUM]
This is a compulsory parameter for the interaction energy evaluation (see f[FORMAT] option), it is required to know which residue
(ligand) the energy has to be computed referred to. You can specify the residue number
only or residue name and reside number (e.g e 9999 or e THA:999).
If you use e without any argument, VEGA uses the default residue number stored in
the prefs file (usually 9999).
3.7 -f[OUTPUT_FORMAT]
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). OUTPUT_FORMAT is a case-insensitive keyword that indicates the
format as shown in the following tables:
Keyword |
Description |
CVFF |
Evaluation of interaction energy (see section 3.7.3). |
INFO |
Information about the molecule (see section 3.7.4). |
3.7.1.1 Evaluation of interaction energy
VEGA can evaluate the ligand-biomacromolecule interaction energy through the molecular
mechanics calculation of non-bond term (R6-R12 Lennard-Johnes) and
coulombic term. At the present time, only the CVFF force field is implemented. Please
remember that ligand and receptor must have the force field and atomic charges correctly
assigned (see p and c options). For the energy evaluation, 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 file) the total interaction energy, its
components (non-bond and coulombic energies) and a table with receptor residues that have
a partial interaction energy greater than 1% of the total energy. This threshold can be
changed in the preference file (see section 5).
3.7.1.2 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),
polypeptidic charge (only for proteins, its calculated at physiological pH on the
basis of aminoacidic composition), aminoacidic or nucleotidic composition:
******************************
**** Infos about molecule ****
******************************
Atoms..............: 48
Heavy atoms........: 25
Residues...........: 1
Molecules..........: 1
Waters.............: 0
Molecular weight...: 345.384 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)
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
If the molecule is a protein or a nucleic acid, the following data are showed:
...
Total charge.......: -23.0004
Polypeptidic 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
Keyword |
Description |
BIOSYM |
New Biosym .car file (archive 3) |
CRD |
MSI CHARMm text file format. |
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. |
GROMOS |
This is the special file format of the molecular mechanics package Gromos. |
GROMOSNM |
GROMOS with the coordinates in nano meters. |
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). |
MOL2 |
Tripos Sybyl Mol 2 file format. |
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. |
OLDBIOSYM |
Old Biosym .car file (archive 1) |
PDB |
PDB full standard (default) |
PDBF |
PDB full standard with special records to include atomic charges and force field parameters, Its totally compatible with the PDB standard, because the extra information are placed in REMARK records. |
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 |
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. Its a sequence of single precision floats with the endian of the computer system that have generated it. |
CSV |
ASCII text file with each field separated by a semicolon. |
QUANTAPLT |
MSI Quanta binary plot file. |
3.7.4 Surface 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 |
BIOSYMSRF |
Text |
Van Der Waals and accessible to solvent molecular surface for Insight II package. |
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 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 Å2. See s[POINTS] option to change this value.
* Available only in full release of VEGA.
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 colouring method. |
VRMLCPK |
VRML 1.0 CPK rappresentation with standard colouring method. |
VRMLPTS |
VRML 1.0 dotted surface rappresentation. |
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).
3.8 g[RADIUS]
If you want calculate a surface map with a probe radius different than the default one
(the default value is the 1.4Å 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.
3.9 i[SHELL RAD SHAPE]
VEGA can solvate a molecule virtually with any type of solvent (e.g. H2O, CCl4,
etc). A special PDB file must be placed in Data/Clusters (Data\Clusters) directory.
This is a solvent assembly with cubic form (usually with dimension of 50x50x50 Å ),
optimized, with uppercase file name and lowercase file extension (e.g. WATER.pdb).
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.
3.10 k[KEYWORDS]
This option is useful to pass the control keywords when a Mopac input file is generated (-f MOPINT option). Remember to use quotas (") if
the number of keyword is more than one. In the prefs file, you can specify the
default Mopac keyword.
3.11 m[KEYWORDS]
This option is needed if you want make a specific measure in a molecular dynamic
trajectory file. You must specify a keyword to set the type of measure and
eventually the atom selection:
Keyword | Description |
ANGLE A1 A2 A3 | Bond angle. |
DISTANCE A1 A2 | Bond length. |
DIPOLE | Molecular dipolar moment. |
SURFACE A1 ... | Surface area. |
SURFDIA A1 ... | Surface diameter. It's the diameter of a theoretical sphere with the surface area of the molecule. |
PLANEANG A1 A2 A3 A4 A5 A6 | Angle between planes defined by A1, A2, A3 and A4, A5, A6. |
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. |
* Available only in full release of VEGA.
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 showed 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 polipeptidic 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.
3.12 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.
3.13 -o[OUTPUT]
With o parameter, you can specify the name of the output file with or without
extension. If the filename doesnt 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 showed in
the following table:
Extension |
Type |
Added |
File Format |
.arc |
T |
N |
Mopac optimized internal coordinates |
.car |
T |
Y |
MSI/Biosym CAR file (old and new subformat) |
.cor |
T |
Y |
MSI/Biosym CAR file with optimized coordinates |
.crd |
T |
Y |
MSI CHARMm |
.cssr |
T |
Y |
Cambridge Data File (CSSR) |
.dat |
T |
Y |
Mopac internal coordinates |
.dcd |
B |
Y |
MSI CHARMm trajectory file |
.ene |
T |
N |
MSI CHARMm energy file |
.ene |
T |
Y |
VEGA interaction energy file |
.ent |
T |
N |
PDB |
.fas |
T |
Y |
FASTA |
.gro |
T |
Y |
Gromos |
.iff |
B |
Y |
Interchange File Format |
.inf |
T |
Y |
VEGA information file |
.mol2 |
T |
Y |
Tripos Sybyl Mol 2 |
.msf |
B |
Y |
MSI Quanta |
.par |
T |
N |
VEGA parameters |
.pdb |
T |
Y |
PDB, PDBF and PDBQ |
.qmc |
T |
N |
QMC (CSSR like format) |
.srf |
B |
Y |
MSI Quanta surface |
.srf |
T |
Y |
MSI/Biosym Insight II surface |
.tem |
T |
N |
VEGA template |
.wrl |
T |
Y |
VRML (Virtual Reality Markup Language) |
.xyz |
T |
Y |
XYZ |
Where the column Extension is the file extension, Type is
the file type (T = text, B = binary), Added 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
(e.g gzip, compress, etc). Redirection is possible with text file formats only.
3.14 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, see section
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.
3.15 r
This switch removes all hydrogen atoms and its very useful to create a PDB file
suitable for uploading to molecular databases.
3.16 -s[POINTS]
With this parameter you can change the point density of a surface map. POINTS is the
number of points per surface unit (Å2). The default value is stored in the prefs
file and usually it is set to 10. For more information about surface calculation, please
consult the section
(-f[FORMAT] option).
3.17 -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.