Trajectory-server

Navigation: Documentation / Commands / topcrd2crd

---

topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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: crd - amber restart file xyz - xyz file (Default: crd)

-o, --output FORMAT specify output format for coordinates: 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 (Default: pdb)

-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: none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names (Default: pdb)

--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 / topcrd2crd

---

topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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: crd - amber restart file xyz - xyz file (Default: crd)

-o, --output FORMAT specify output format for coordinates: 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 (Default: pdb)

-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: none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names (Default: pdb)

--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

---

topcut: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

blur: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

treshold filter treshold value

output output result file or - for result printed to standard output

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

---

cats: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / d2u

---

d2u: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / gauss-aw-gen

---

gauss-aw-gen: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-r, --stop REAL right boundary of integration interval (Default: 1)

-p, --polynom NAME name of orthogonal polynom: legendre (Default: legendre)

-o, --output NAME output format: abscissas, weights, or both (Default: both)

--noheader do not print header to output

--reverse print results in reverse order

--af FORMAT output FORMAT of abscissas values (Default: %15.7e)

--wf FORMAT output FORMAT of weights error values (Default: %15.6e)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / gauss-integrate

---

gauss-integrate: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-r, --stop REAL right boundary of integration interval (Default: 1)

--offset REAL specify integration constant (Default: 0)

-p, --polynom NAME name of orthogonal polynom: legendre (Default: legendre)

--progress show integration progress

--noheader do not print header to output

--nosigma standard deviation of derivative is not present in input data

--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

Navigation: Documentation / Commands / histogram

---

histogram: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-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)

-l, --start REAL REAL is the left value of the histogram interval (Default: 0)

-r, --stop REAL REAL is the right value of the histogram interval (Default: 0)

--nbins NUM NUM is the number of histogram bins (Default: 40)

-n, --normalize normalize histogram

--fx FORMAT output FORMAT of X values (Default: %15.7e)

--fn FORMAT output FORMAT of N(X) values (Default: %15d)

--fr FORMAT output FORMAT of r(X) values (Default: %14.6e)

--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

---

integrate: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / pdb2fasta

---

pdb2fasta: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / propsum

---

propsum: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

--intermediates print running intermediates

--noheader do not print header for running intermediates

--fn FORMAT output FORMAT of the number of X values (Default: %15d)

--fx FORMAT output FORMAT of echoed X values (Default: %15.7e)

--fsum FORMAT output FORMAT of sum(X) values (Default: %14.6e)

--fave FORMAT output FORMAT of ave(X) values (Default: %15.7e)

--frmsd FORMAT output FORMAT of RMSD(X) values (Default: %14.6e)

--fsigma FORMAT output FORMAT of sigma() values (Default: %14.6e)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / svs-client

---

vs-client: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

-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

---

svs-project-add-structures: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-p, --progress print progress

-u, --usehiearchy use hiearchy

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / svs-project-alter

---

svs-project-alter: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

svs-project-create: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

svs-project-info: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

svs-project-sql: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / svs-server

---

vs-server: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

mol-split: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-o, --outformat FORMAT output molecule format (Default: xyz)

-a, --unisID NAME UNIS type (four characters) with autoindexing or 'title' for UNIS ID extracted from molecule title (Default: UNIS)

-l, --lineentries read as line entries

-c, --createhiearchy create directory hiearchy

-d, --printduplicit print IDs of duplicit molecules

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / top2delphi

---

top2delphi: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

top2params: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

topcharges: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

--setcharges FILE set charges from FILE

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topcrd2crd

---

topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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: crd - amber restart file xyz - xyz file (Default: crd)

-o, --output FORMAT specify output format for coordinates: 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 (Default: pdb)

-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: none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names (Default: pdb)

--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

---

topcrd2mmcom: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

COMOUT output gaussian input file

Options

-m, --mask MASK definition of high ONIOM layer from mask definition

-f, --maskfile MASKFILE definition of high ONIOM layer from mask definition stored in file

--scee REAL scaling factor for 1-4 electrostatic interactions (Default: 1.2)

--scnb REAL scaling factor for 1-4 van der Waals interactions (Default: 2)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topcut

---

topcut: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

topinfo: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

topjoinmol: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topmask

---

topmask: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topmask

Synopsis

topmask [OPTIONS] [--] PARM MASK

Description

Print the names of atoms or residues selected by the application of MASK. Current implementation fully supports ambmask syntax (see AMBER manual).

Arguments

PARM topology file name. If - is provided then topology is read from standard input stream.

MASK mask specification

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.

-r, --residues perform selection on the level of residues. The mask specification cannot contains atom selectors (@ @ @%).

-o, --output FORMAT specify output format. Default format 'cats' prints atoms or residues as the list sorted into three colums. Format 'list' prints the same information as 'cats' but only to a single colum without any header. Format 'number' prints only the number of selected atoms or residues. Format 'amber' provides the same output as ambmask. Format 'bmask' write bitmap mask. (Default: cats)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topremixlj

---

topremixlj: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topremixlj

Synopsis

topremixlj [OPTIONS] [--] INPUT OUTPUT

Description

Remix Lennard-Jones pair parameters.

Arguments

INPUT input topology name, if '-' is provided then the topology is read from the standard input stream.

OUTPUT output topology name, if '-' is provided then the topology is written to the standard output stream.

Options

-r, --rule TYPE combining rule: LB (Lorentz-Berthelot), KG (Kong), WH (Waldman-Hagler) (Default: LB)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topsolsol

---

topsolsol: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topsolsol

Synopsis

topsolsol [OPTIONS] [--] PARM TRIANGULATION SOLUTE SOLVENT OUTPUT

Description

Analyse solute/solvent contacts according to Delaunay triangulation among the system atoms. The solvent residues are discrimated into directly bound, first, second, third, and fourth solvation layers. The tringulation is created as follows:

topcrd2crd --output rbox topology.parm7 coords.rst7 coords.rbox
cat coords.rbox | qdelaunay i TO output

Arguments

PARM topology file name

TRIANGULATION file name with Delaunay triangulation of the system created by qdelaunay command from QHull package

SOLUTE solute definition in ASL mask format

SOLVENT solvent definition in ASL mask format

OUTPUT file name with output masks defining solvent layers around solute

Options

-r, --ratio DOUBLE directly bound solvent ratio (Default: 0.2)

--directnotsolvent do not use direct as solvent

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / trajectory-client

---

trajectory-client: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

trajectory-client

Synopsis

trajectory-client [OPTIONS] [--] trj://server[:port]/command

Description

This program interacts with a trajectory server.

Arguments

trj://server[:port]/command specifies fully qualified administration request. Trasport protocol cats:// has to be always specified. It is followed by server parameter which could be either DNS name or IP address of server. Optional port parameter is port number used in a communication. Finally, the command is a task, which can be one of the following: register = register client on server side unregister = unregister client on server side (unregister?id=client_id) getcrd = get coordinate snapshot (getcrd?id=client_id,topology=file1.top,coords=file2.crd) getvel = get velocities (getvel?id=client_id,topology=file1.top,coords=file2.crd) info = prints information about registered clients shutdown = stops server execution errors = prints errors from 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

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / trajectory-server

---

trajectory-server: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

trajectory-server

Synopsis

trajectory-server [OPTIONS] [--] control

Description

trajectory-server extracts snapshots from given AMBER trajectories on the demand of trajectory-client command.

Arguments

control name of control file or - for data from standard input

Options

--donotshutdown do not shutdown automatically when all clients are unregistered

--notrajinfo do not print info about trajectory

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / u2d

---

u2d: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

u2d

Synopsis

u2d [OPTIONS] [--] FILE1 [FILE2 ...]

Description

Converts given file(s) from UNIX (\n) to DOS (\r\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

Navigation: Documentation / Commands / xyzfit

---

xyzfit: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

xyzfit

Synopsis

xyzfit [OPTIONS] [--] ref str [out]

Description

Calculate RMSD between two molecules.

ref - name of reference molecule file or - for input from standard input stream
str - name of super-imposed molecule file or - for input from standard input stream
out - super-imposed structure

Options

--refformat FORMAT format of reference molecule (Default: auto)

--strformat FORMAT format of superimposed molecule (Default: auto)

--pattern atom map between reference and superimposed molecule [num1:num2,..] or identity

--nofit do not fit molecules

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / xyzsplit

---

xyzsplit: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

xyzsplit

Synopsis

xyzsplit [OPTIONS] [--] STRUCTURE

Description

Split the structure read from the XYZ file into individual molecules.

Arguments

STRUCTURE Structure in the xyz format. If the name is '-' then the structure is read from the standard input.

Options

--cp save structures in the format for CP correction (orca)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands

• blur
• cats
• d2u
• gauss-aw-gen
• gauss-integrate
• histogram
• integrate
• pdb2fasta
• propsum
• svs-client
• svs-project-add-structures
• svs-project-alter
• svs-project-create
• svs-project-info
• svs-project-sql
• svs-server
• svs-split-mol
• top2delphi
• top2params
• topcharges
• topcrd2crd
• topcrd2mmcom
• topcut
• topinfo
• topjoinmol
• topmask
• topremixlj
• topsolsol
• trajectory-client
• trajectory-server
• u2d
• xyzfit
• xyzsplit

Navigation: Documentation / Commands / blur

---

blur: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

treshold filter treshold value

output output result file or - for result printed to standard output

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

---

cats: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / d2u

---

d2u: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / gauss-aw-gen

---

gauss-aw-gen: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-r, --stop REAL right boundary of integration interval (Default: 1)

-p, --polynom NAME name of orthogonal polynom: legendre (Default: legendre)

-o, --output NAME output format: abscissas, weights, or both (Default: both)

--noheader do not print header to output

--reverse print results in reverse order

--af FORMAT output FORMAT of abscissas values (Default: %15.7e)

--wf FORMAT output FORMAT of weights error values (Default: %15.6e)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / gauss-integrate

---

gauss-integrate: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-r, --stop REAL right boundary of integration interval (Default: 1)

--offset REAL specify integration constant (Default: 0)

-p, --polynom NAME name of orthogonal polynom: legendre (Default: legendre)

--progress show integration progress

--noheader do not print header to output

--nosigma standard deviation of derivative is not present in input data

--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

Navigation: Documentation / Commands / histogram

---

histogram: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-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)

-l, --start REAL REAL is the left value of the histogram interval (Default: 0)

-r, --stop REAL REAL is the right value of the histogram interval (Default: 0)

--nbins NUM NUM is the number of histogram bins (Default: 40)

-n, --normalize normalize histogram

--fx FORMAT output FORMAT of X values (Default: %15.7e)

--fn FORMAT output FORMAT of N(X) values (Default: %15d)

--fr FORMAT output FORMAT of r(X) values (Default: %14.6e)

--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

---

integrate: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / pdb2fasta

---

pdb2fasta: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / propsum

---

propsum: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

--intermediates print running intermediates

--noheader do not print header for running intermediates

--fn FORMAT output FORMAT of the number of X values (Default: %15d)

--fx FORMAT output FORMAT of echoed X values (Default: %15.7e)

--fsum FORMAT output FORMAT of sum(X) values (Default: %14.6e)

--fave FORMAT output FORMAT of ave(X) values (Default: %15.7e)

--frmsd FORMAT output FORMAT of RMSD(X) values (Default: %14.6e)

--fsigma FORMAT output FORMAT of sigma() values (Default: %14.6e)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / svs-client

---

vs-client: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

-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

---

svs-project-add-structures: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-p, --progress print progress

-u, --usehiearchy use hiearchy

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / svs-project-alter

---

svs-project-alter: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

svs-project-create: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

svs-project-info: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

svs-project-sql: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

Navigation: Documentation / Commands / svs-server

---

vs-server: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

mol-split: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-o, --outformat FORMAT output molecule format (Default: xyz)

-a, --unisID NAME UNIS type (four characters) with autoindexing or 'title' for UNIS ID extracted from molecule title (Default: UNIS)

-l, --lineentries read as line entries

-c, --createhiearchy create directory hiearchy

-d, --printduplicit print IDs of duplicit molecules

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / top2delphi

---

top2delphi: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

top2params: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

---

topcharges: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

--setcharges FILE set charges from FILE

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topcrd2crd

---

topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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: crd - amber restart file xyz - xyz file (Default: crd)

-o, --output FORMAT specify output format for coordinates: 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 (Default: pdb)

-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: none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names (Default: pdb)

--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

---

topcrd2mmcom: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

COMOUT output gaussian input file

Options

-m, --mask MASK definition of high ONIOM layer from mask definition

-f, --maskfile MASKFILE definition of high ONIOM layer from mask definition stored in file

--scee REAL scaling factor for 1-4 electrostatic interactions (Default: 1.2)

--scnb REAL scaling factor for 1-4 van der Waals interactions (Default: 2)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topcut

---

topcut: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

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topinfo: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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

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topjoinmol: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topmask

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topmask: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topmask

Synopsis

topmask [OPTIONS] [--] PARM MASK

Description

Print the names of atoms or residues selected by the application of MASK. Current implementation fully supports ambmask syntax (see AMBER manual).

Arguments

PARM topology file name. If - is provided then topology is read from standard input stream.

MASK mask specification

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.

-r, --residues perform selection on the level of residues. The mask specification cannot contains atom selectors (@ @ @%).

-o, --output FORMAT specify output format. Default format 'cats' prints atoms or residues as the list sorted into three colums. Format 'list' prints the same information as 'cats' but only to a single colum without any header. Format 'number' prints only the number of selected atoms or residues. Format 'amber' provides the same output as ambmask. Format 'bmask' write bitmap mask. (Default: cats)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topremixlj

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topremixlj: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topremixlj

Synopsis

topremixlj [OPTIONS] [--] INPUT OUTPUT

Description

Remix Lennard-Jones pair parameters.

Arguments

INPUT input topology name, if '-' is provided then the topology is read from the standard input stream.

OUTPUT output topology name, if '-' is provided then the topology is written to the standard output stream.

Options

-r, --rule TYPE combining rule: LB (Lorentz-Berthelot), KG (Kong), WH (Waldman-Hagler) (Default: LB)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / topsolsol

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topsolsol: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topsolsol

Synopsis

topsolsol [OPTIONS] [--] PARM TRIANGULATION SOLUTE SOLVENT OUTPUT

Description

Analyse solute/solvent contacts according to Delaunay triangulation among the system atoms. The solvent residues are discrimated into directly bound, first, second, third, and fourth solvation layers. The tringulation is created as follows:

topcrd2crd --output rbox topology.parm7 coords.rst7 coords.rbox
cat coords.rbox | qdelaunay i TO output

Arguments

PARM topology file name

TRIANGULATION file name with Delaunay triangulation of the system created by qdelaunay command from QHull package

SOLUTE solute definition in ASL mask format

SOLVENT solvent definition in ASL mask format

OUTPUT file name with output masks defining solvent layers around solute

Options

-r, --ratio DOUBLE directly bound solvent ratio (Default: 0.2)

--directnotsolvent do not use direct as solvent

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / trajectory-client

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trajectory-client: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

trajectory-client

Synopsis

trajectory-client [OPTIONS] [--] trj://server[:port]/command

Description

This program interacts with a trajectory server.

Arguments

trj://server[:port]/command specifies fully qualified administration request. Trasport protocol cats:// has to be always specified. It is followed by server parameter which could be either DNS name or IP address of server. Optional port parameter is port number used in a communication. Finally, the command is a task, which can be one of the following: register = register client on server side unregister = unregister client on server side (unregister?id=client_id) getcrd = get coordinate snapshot (getcrd?id=client_id,topology=file1.top,coords=file2.crd) getvel = get velocities (getvel?id=client_id,topology=file1.top,coords=file2.crd) info = prints information about registered clients shutdown = stops server execution errors = prints errors from 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

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit

Navigation: Documentation / Commands / trajectory-server

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trajectory-server: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

trajectory-server

Synopsis

trajectory-server [OPTIONS] [--] control

Description

trajectory-server extracts snapshots from given AMBER trajectories on the demand of trajectory-client command.

Arguments

control name of control file or - for data from standard input

Options

--donotshutdown do not shutdown automatically when all clients are unregistered

--notrajinfo do not print info about trajectory

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit