topjoinmol
Navigation: Documentation / Commands / topcrd2crd
Name
topcrd2crd
Synopsis
topcrd2crd [OPTIONS] [--] PARM CRD OUT
Description
Converts AMBER topology and coordinates to coordinates in other format.
Arguments
| PARM topology file name
|
| CRD input coordinates file name or - for standard input
|
| OUT output coordinates file name or - for standard output
|
Options
| -i, --input FORMAT specify input format for coordinates: (Default: crd)
crd - amber restart file xyz - xyz file |
| -o, --output FORMAT specify output format for coordinates: (Default: pdb)
crd - amber restart file pdb - PDB file pqr - PDB file with atomic radii and charges xyz - xyz file xyzr - xyz file with atomic radii com - gaussian input file rbox - rbox format for qhull traj - amber trajectory file adf - plain ADF input adffrag - plain ADF input with one fragment adf3drism - plain ADF input for 3D-RISM |
| -m, --mask MASK only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.
|
| -f, --maskfile MASKFILE only atoms selected according to the mask will be converted. The mask specification is read from the first line of the file of name MASKFILE. This option is suitable for the specification of very long masks. Mutually exclusive with 'mask' option.
|
| -t, --mangle FORMAT specify atom names mangling scheme: (Default: pdb)
none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names |
| --rscale scale factor for atomic radii (r_new = r * scale + offset)
|
| --roffset offset for atomic radii (r_new = r * scale + offset)
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| -r, --reindex reindex atom and residue numbers counting from 1
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| --copybox copy box information to output file
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| --novelocities do not transfer velocities
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| --nochains do not print chain IDs into pdb files
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / topcrd2crd
Name
topcrd2crd
Synopsis
topcrd2crd [OPTIONS] [--] PARM CRD OUT
Description
Converts AMBER topology and coordinates to coordinates in other format.
Arguments
| PARM topology file name
|
| CRD input coordinates file name or - for standard input
|
| OUT output coordinates file name or - for standard output
|
Options
| -i, --input FORMAT specify input format for coordinates: (Default: crd)
crd - amber restart file xyz - xyz file |
| -o, --output FORMAT specify output format for coordinates: (Default: pdb)
crd - amber restart file pdb - PDB file pqr - PDB file with atomic radii and charges xyz - xyz file xyzr - xyz file with atomic radii com - gaussian input file rbox - rbox format for qhull traj - amber trajectory file adf - plain ADF input adffrag - plain ADF input with one fragment adf3drism - plain ADF input for 3D-RISM |
| -m, --mask MASK only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.
|
| -f, --maskfile MASKFILE only atoms selected according to the mask will be converted. The mask specification is read from the first line of the file of name MASKFILE. This option is suitable for the specification of very long masks. Mutually exclusive with 'mask' option.
|
| -t, --mangle FORMAT specify atom names mangling scheme: (Default: pdb)
none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names |
| --rscale scale factor for atomic radii (r_new = r * scale + offset)
|
| --roffset offset for atomic radii (r_new = r * scale + offset)
|
| -r, --reindex reindex atom and residue numbers counting from 1
|
| --copybox copy box information to output file
|
| --novelocities do not transfer velocities
|
| --nochains do not print chain IDs into pdb files
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / topcut
Name
topcut
Synopsis
topcut [OPTIONS] [--] OLD MASK NEW
Description
Cut AMBER topology and saves it as new one. Artifical topologies with open valences could be save too but use them only for visualisation purposes not for energy evaluation.
Arguments
| OLD old topology name. If - is provided then topology is read from standard input stream.
|
| MASK mask specification
|
| NEW new topology name. If - is provided then topology is written to standard output stream.
|
Options
| -c, --coords CRD optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)
|
| -f, --maskfile read mask specification from the first line of the file of name MASK. This option is suitable for the specification of very long masks.
|
| --copybox copy old box information to new topology
|
| --ignoreerrors ignore open valences in newly created topology
|
| --ver6 save new topology in version AMBER 6
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / blur
Name
blur
Synopsis
blur [OPTIONS] [--] input treshold output
Description
Blur 3D-density map in X-Plore format by data filtering in reciprocal Fourier space.
Arguments
| input input data file or - for data taken from standard input
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| treshold filter treshold value
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| output output result file or - for result printed to standard output
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Options
| -f, --filter STRING filter type: either low-pass or gauss is implemeted (Default: low-pass)
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / cats
Name
cats
Synopsis
cats [OPTIONS] [--] [SCRIPT] [ARG1 [ARG2] ...]
Description
CATs QScript interpretter.
Arguments:
SCRIPT file to be interpreted
Options
| -i, --interactive run in interactive mode
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / d2u
Name
d2u
Synopsis
d2u [OPTIONS] [--] FILE1 [FILE2 ...]
Description
d2u converts given file(s) from DOS (\r\n) to UNIX (\n) end line character style.
Arguments:
FILE1 file to be converted or - for conversion from standard input to standard output
Options
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / gauss-aw-gen
Name
gauss-aw-gen
Synopsis
gauss-aw-gen [OPTIONS] [--] N output
Description
Numerically determines abscissas and weights used in Gaussian quadrature.
Arguments
| N number of points used in Gaussian quadrature
|
| output output result file or - for results printed to standard output
|
Options
| -l, --start REAL left boundary of integration interval (Default: 0)
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| -r, --stop REAL right boundary of integration interval (Default: 1)
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| -p, --polynom NAME name of orthogonal polynom: legendre (Default: legendre)
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| -o, --output NAME output format: abscissas, weights, or both (Default: both)
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| --noheader do not print header to output
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| --reverse print results in reverse order
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| --af FORMAT output FORMAT of abscissas values (Default: %15.7e)
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| --wf FORMAT output FORMAT of weights error values (Default: %15.6e)
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / gauss-integrate
Name
gauss-integrate
Synopsis
gauss-integrate [OPTIONS] [--] N input output
Description
Numerically integrate data using Gaussian quadrature.
Arguments
| N number of points used in Gaussian quadrature
|
| input input data file or - for data taken from standard input
|
| output output result file or - for results printed to standard output
|
Options
| -l, --start REAL left boundary of integration interval (Default: 0)
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| -r, --stop REAL right boundary of integration interval (Default: 1)
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| --offset REAL specify integration constant (Default: 0)
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| -p, --polynom NAME name of orthogonal polynom: legendre (Default: legendre)
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| --progress show integration progress
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| --noheader do not print header to output
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| --nosigma standard deviation of derivative is not present in input data
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| --fx FORMAT output FORMAT of echoed x values (Default: %15.7e)
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| --fy FORMAT output FORMAT of echoed derivative values (Default: %15.7e)
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| --fs FORMAT output FORMAT of echoed sigma values (Default: %14.6e)
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| --fi FORMAT output FORMAT of integrated values (Default: %15.7e)
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| --fe FORMAT output FORMAT of integrated error values (Default: %14.6e)
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / histogram
Name
histogram
Synopsis
histogram [OPTIONS] [--] input output
Description
Perform histogram analysis.
Arguments
| input input data file or - for data taken from standard input
|
| output output result file or - for result printed to standard output
|
Options
| -s, --skip LINES number of lines skipped from the beginning of input file (Default: 0)
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| -a, --anal LINES number of LINES from input file to be analyzed (Default: -1)
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| -p, --pad LINES number of padding LINES between used records from input file (Default: 0)
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| -c, --column NUM NUM is the index of column to be analyzed (Default: 1)
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| -l, --start REAL REAL is the left value of the histogram interval (Default: 0)
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| -r, --stop REAL REAL is the right value of the histogram interval (Default: 0)
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| --nbins NUM NUM is the number of histogram bins (Default: 40)
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| -n, --normalize normalize histogram
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| --fx FORMAT output FORMAT of X values (Default: %15.7e)
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| --fn FORMAT output FORMAT of N(X) values (Default: %15d)
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| --fr FORMAT output FORMAT of r(X) values (Default: %14.6e)
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| --noheader do not print header to output
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / integrate
Name
integrate
Synopsis
integrate [OPTIONS] [--] input output
Description
Integrate numerically given data by Simpson method. Program reads three numbers from input file (x coordinate, derivative, and standard deviation of derivative). As output program prints copy of input data plus integrated values and its standard error.
Arguments
| input input data file or - for data taken from standard input
|
| output output result file or - for result printed to standard output
|
Options
| --offset REAL specify integration constant (Default: 0)
|
| -s, --skip LINES number of lines skipped from the beginning of input file (Default: 0)
|
| -a, --anal LINES number of LINES from input file to be analyzed (Default: -1)
|
| -p, --pad LINES number of padding LINES between used records from input file (Default: 0)
|
| --nosigma standard deviation of derivative is not present in input data
|
| --noheader do not print header to output
|
| --fx FORMAT output FORMAT of echoed x values (Default: %15.7e)
|
| --fy FORMAT output FORMAT of echoed derivative values (Default: %15.7e)
|
| --fs FORMAT output FORMAT of echoed sigma values (Default: %14.6e)
|
| --fi FORMAT output FORMAT of integrated values (Default: %15.7e)
|
| --fe FORMAT output FORMAT of integrated error values (Default: %14.6e)
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / pdb2fasta
Name
pdb2fasta
Synopsis
pdb2fasta [OPTIONS] [--] input output
Description
Extracts FASTA sequences of all chains from PDB file.
Arguments
| input input pdb file or - for data taken from standard input
|
| output output file with FASTA sequences or - for result printed to standard output
|
Options
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / propsum
Name
propsum
Synopsis
propsum [OPTIONS] [--] input
Description
Calculate total sum of value X, its average , root-mean-square deviation of X, and standard deviation of .
Arguments
| input input data file or - for data taken from standard input
|
Options
| -s, --skip LINES number of lines skipped from the beginning of input file (Default: 0)
|
| -a, --anal LINES number of LINES from input file to be analyzed (Default: -1)
|
| -p, --pad LINES number of padding LINES between used records from input file (Default: 0)
|
| -c, --column NUM NUM is the index of column to be analyzed (Default: 1)
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| --intermediates print running intermediates
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| --noheader do not print header for running intermediates
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| --fn FORMAT output FORMAT of the number of X values (Default: %15d)
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| --fx FORMAT output FORMAT of echoed X values (Default: %15.7e)
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| --fsum FORMAT output FORMAT of sum(X) values (Default: %14.6e)
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| --fave FORMAT output FORMAT of ave(X) values (Default: %15.7e)
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| --frmsd FORMAT output FORMAT of RMSD(X) values (Default: %14.6e)
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| --fsigma FORMAT output FORMAT of sigma() values (Default: %14.6e)
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / svs-client
Name
vs-client
Synopsis
vs-client [OPTIONS] [--] svs://server[:port]/command
Description
Client of the server/client virtual screening infrastructure.
Arguments
| svs://server[:port]/command Specifies fully qualified administration request. Trasport protocol svs:// has to be always specified, which is followed by the server specification (DNS name or IP address of the server and optionally by the server port). This is followed by the command, which can be one of the following:
register = register client on server side unregister = unregister client on server side (unregister?id=client_id) get = get unprocessed structure from database (get?id=client_id,structure=file.ext[,type=xyz]) write = write data to database and set structure as processed (write?id=client_id,molid=molecule_id[,structure=file.ext,type=log]) load = load structure from database (load?id=client_id,molid=molecule_id[,structure=file.ext,type=xyz]) save = save structure to database (save?id=client_id,molid=molecule_id[,structure=file.ext,type=log]) installpkg = install client package to current directory appname = get client application name info = prints information about registered clients shutdown = stops server execution errors = prints errors from the server stack |
Options
| -s, --serverkey FILE name of file containing server description (name, port, and password) (mutually exclusive with 'password' option)
|
| -p, --password FILE name of file containing server magic word, if not specified then password is read interactively
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / svs-project-add-structures
Name
svs-project-add-structures
Synopsis
svs-project-add-structures [OPTIONS] [--] structuredb projectdb
Description
Initialize the project database by records from the structure database.
Arguments
| structuredb pathname to the structure database
|
| projectdb filename with the project database
|
Options
| -i, --input FORMAT input molecule format (Default: xyz)
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| -p, --progress print progress
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| -u, --usehiearchy use hiearchy
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / svs-project-alter
Name
svs-project-alter
Synopsis
svs-project-alter [OPTIONS] [--] projectdb command
Description
Alter a project setup.
Arguments
| projectdb filename with the project database
|
| command Supported commands:
softreset = set processing items into unprocessed state hardreset = set all items into unprocessed state finalizeall = set all items into processed state addindx = add primary index to the ID column removeindx = remove primary index from the ID solumn rebuildindx = removeindx + addindx deleteall = delete all records from project database |
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / svs-project-create
Name
svs-project-create
Synopsis
svs-project-create [OPTIONS] [--] projectdb
Description
Create a new virtual screening project.
Arguments
| projectdb filename with the project database
|
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / svs-project-info
Name
svs-project-info
Synopsis
svs-project-info [OPTIONS] [--] projectdb
Description
Print information about the project.
Arguments
| projectdb filename with the project database
|
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / svs-project-sql
Name
svs-project-sql
Synopsis
svs-project-sql [OPTIONS] [--] [projectdb ...]
Description
SQL command line interface to virtual screening projects.
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / svs-server
Name
vs-server
Synopsis
vs-server [OPTIONS] [--] control
Description
Server of the server/client virtual screening infrastructure.
Arguments
| control name of control file or - for data from the standard input
|
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / svs-split-mol
Name
mol-split
Synopsis
mol-split [OPTIONS] [--] input structuredb
Description
Split a multiple structure file into individual structures. The input file can be processed either by openbalel (--format auto or user specified input format) or by a special parser (--lineentries) in the case of ssmi (stream SMILE file). The format ssmi contains two entries on every line. The first entry is an ID of molecule and the second entry is SMILE representation of a molecule.
Arguments
| input name of input file or - for input from the standard input stream
|
| structuredb pathname to the structure database
|
Options
| -f, --informat FORMAT input molecule format (Default: auto)
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| -o, --outformat FORMAT output molecule format (Default: xyz)
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| -a, --unisID NAME UNIS type (four characters) with autoindexing or 'title' for UNIS ID extracted from molecule title (Default: UNIS)
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| -l, --lineentries read as line entries
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| -c, --createhiearchy create directory hiearchy
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| -d, --printduplicit print IDs of duplicit molecules
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
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Navigation: Documentation / Commands / top2delphi
Name
top2delphi
Synopsis
top2delphi [OPTIONS] [--] TOPOLOGY RADII CHARGES
Description
Extract radii and charges information in DELPHI format from AMBER topology.
Arguments
| TOPOLOGY topology name. If - is provided then topology is read from standard input stream.
|
| RADII radii file name
|
| CHARGES charges file name
|
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / top2params
Name
top2params
Synopsis
top2params [OPTIONS] [--] TOPOLOGY PARAMS
Description
Extract force field information from given topology.
Arguments
| TOPOLOGY topology name. If - is provided then topology is read from standard input stream.
|
| PARAMS parameter file name. If - is provided then parameters are written to standard output stream.
|
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / topcharges
Name
topcharges
Synopsis
topcharges [OPTIONS] [--] TOP OUT
Description
Manipulate with topology charges.
Arguments
| TOP topology name. If - is provided then topology is read from standard input stream.
|
| OUT output file name. If - is provided then output is written to standard output stream.
|
Options
| -m, --mask MASK only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.
|
| -f, --maskfile MASKFILE only atoms selected according to the mask will be converted. The mask specification is read from the first line of the file of name MASKFILE. This option is suitable for the specification of very long masks. Mutually exclusive with 'mask' option.
|
| --getcharges get topology charges
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| --setcharges FILE set charges from FILE
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / topcrd2crd
Name
topcrd2crd
Synopsis
topcrd2crd [OPTIONS] [--] PARM CRD OUT
Description
Converts AMBER topology and coordinates to coordinates in other format.
Arguments
| PARM topology file name
|
| CRD input coordinates file name or - for standard input
|
| OUT output coordinates file name or - for standard output
|
Options
| -i, --input FORMAT specify input format for coordinates: (Default: crd)
crd - amber restart file xyz - xyz file |
| -o, --output FORMAT specify output format for coordinates: (Default: pdb)
crd - amber restart file pdb - PDB file pqr - PDB file with atomic radii and charges xyz - xyz file xyzr - xyz file with atomic radii com - gaussian input file rbox - rbox format for qhull traj - amber trajectory file adf - plain ADF input adffrag - plain ADF input with one fragment adf3drism - plain ADF input for 3D-RISM |
| -m, --mask MASK only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.
|
| -f, --maskfile MASKFILE only atoms selected according to the mask will be converted. The mask specification is read from the first line of the file of name MASKFILE. This option is suitable for the specification of very long masks. Mutually exclusive with 'mask' option.
|
| -t, --mangle FORMAT specify atom names mangling scheme: (Default: pdb)
none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names |
| --rscale scale factor for atomic radii (r_new = r * scale + offset)
|
| --roffset offset for atomic radii (r_new = r * scale + offset)
|
| -r, --reindex reindex atom and residue numbers counting from 1
|
| --copybox copy box information to output file
|
| --novelocities do not transfer velocities
|
| --nochains do not print chain IDs into pdb files
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / topcrd2mmcom
Name
topcrd2mmcom
Synopsis
topcrd2mmcom [OPTIONS] [--] PARM CRD COMOUT
Description
Convert AMBER topology and coordinates to gaussian input format with MM information. Input is suitable for QM/MM calculation.
Arguments
| PARM topology file name
|
| CRD input coordinates in AMBER coordinate format
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| COMOUT output gaussian input file
|
Options
| -m, --mask MASK definition of high ONIOM layer from mask definition
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| -f, --maskfile MASKFILE definition of high ONIOM layer from mask definition stored in file
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| --scee REAL scaling factor for 1-4 electrostatic interactions (Default: 1.2)
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| --scnb REAL scaling factor for 1-4 van der Waals interactions (Default: 2)
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / topcut
Name
topcut
Synopsis
topcut [OPTIONS] [--] OLD MASK NEW
Description
Cut AMBER topology and saves it as new one. Artifical topologies with open valences could be save too but use them only for visualisation purposes not for energy evaluation.
Arguments
| OLD old topology name. If - is provided then topology is read from standard input stream.
|
| MASK mask specification
|
| NEW new topology name. If - is provided then topology is written to standard output stream.
|
Options
| -c, --coords CRD optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)
|
| -f, --maskfile read mask specification from the first line of the file of name MASK. This option is suitable for the specification of very long masks.
|
| --copybox copy old box information to new topology
|
| --ignoreerrors ignore open valences in newly created topology
|
| --ver6 save new topology in version AMBER 6
|
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / topinfo
Name
topinfo
Synopsis
topinfo [OPTIONS] [--] PARM
Description
Print basic information about AMBER topology.
Arguments
| PARM topology name. If - is provided then topology is read from standard input stream.
|
Options
| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|
Navigation: Documentation / Commands / topjoinmol
Name
topjoinmol
Synopsis
topjoinmol OPTIONS [--] OLD NEW
Description
Change the information about molecules used during pressure scalling.
Arguments
| OLD old topology name. If - is provided then topology is read from standard input stream.
|
| NEW new topology name. If - is provided then topology is written to standard output stream.
|
Options
| -n, --nmol NUM number of molecules to be connected together (Default: 0)
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| -v, --verbose increase output verbosity
|
| --version output version information and exit
|
| -h, --help display this help and exit
|