Home-made programs

Amber

• ambanalys (/teo/ulf/Bin)

Reads Amber pdbout, sander/gibbs.out, mdrest/prest files, md/pcoord files.
Constructs pdb files
Writes out energy statistics of a simulation
Writes out geometry statistics of a simulation (follows distances, hydrogen bonds, and hydrophobic interactions; calculates rms fluctuations.
• changeparm (/teo/bio/Bin)

Reads an Amber parameter file
Writes out a pdb file
Change charges (also zero all)
Calculate all energy components
• changepot
  Reads a Gaussian ESP calculation and constructs input files to an Resp calculation
• comqumtoamber
• modrest

Reads a restart file and modifies it
• pdbtoamber

Reads a pdb file and sets up an Amber calculation (link, edit, parm files)

CNS

• changemtf (/teo/bio/Bin)

Reads a CNS mtf (structure) file
and changes some items (e.g. charge)
• comqumtocns
• describe (/teo/bio/Bin)

Reads pdb, Turbomole, Gaussian, and Mulliken output files
Describes the geometry around an atom (typically a metal)
Describes hydrogen bonds in the system
Describe water interactions
Performs all types of analysis of Hessians (frequency analysis, force constants a la Seminario, CNS parameter and topology files).
• pdbtocnsrefl

Converts a reflection file from pdb to CNS format

ComQum(-X)

• calcwa (/teo/bio/Bin)
• checkcoord (/teo/bio/Bin)
• comqum (/teo/bio/Bin)
• comqumtoamber
• comqumtocns
• comqumtoturbo
• comqumx
• cqtunzip
• cqprep
• cqx_secscript
• cqxback
• cqxprep
• fix
• fixcharge
• fixcharge2_turboin
• fixcharge_amberin
• fixcharge_amberout
• fixcharge_cnsin
• fixcharge_cnsout
• fixcharge_turboin
• fixcoord1
• fixcoord1_amberin
• fixcoord1_amberout
• fixcoord1_cnsin
• fixcoord1_cnsout
• fixcoord1_turboin
• fixcoord2
• fixcoord2_amberin
• fixcoord2_cnsin
• fixcoord2_turbonin
• fixcoord2_turboout
• fixenergy
• fixenergy_amberin
• fixenergy_cnsin
• fixenergy_turboin
• fixenergy_turboout
• fixforce
• fixforce_amberin
• fixforce_cnsin
• fixforce_turboin
• fixforce_turboout
• makechargecorr
• offsetf
• pdbtocomqum

Gaussian

• changemos
• Reads Turbomole mos, alpha, beta, and natural files and onstructs starting orbitals to a Gaussian calculation
• changepdb (/teo/bio/Bin)

Reads a pdb file and writes a Gaussian input file
• changepot
  Reads a Gaussian ESP calculation and constructs input files to an Resp calculation
• checkcharges (/teo/bio/Bin)

Reads in a point charge file and check that the charges sum up to an integer
• compreorg (/teo/bio/Bin)

Reads two describe files with force constant analysis and calculates the reorganisation energy from a harmonic approximation
• describe (/teo/bio/Bin)

Reads pdb, Turbomole, Gaussian, and Mulliken output files
Describes the geometry around an atom (typically a metal)
Describes hydrogen bonds in the system
Describe water interactions
Performs all types of analysis of Hessians (frequency analysis, force constants a la Seminario, CNS parameter and topology files).
• gausstopdb

Constructs a pdb file from the final Gaussian coordinates
• gorbitlas

Writes out the major components of a Gaussian wavefunction
• turbotomolcas
  Reads Turbomole data and constructs Molcas or Gaussian input files

Mead

• changepdb (/teo/bio/Bin)

Reads a pdb file and writes a several types of Mead input file

Molcas

• turbotomolcas
  Reads Turbomole data and constructs Molcas or Gaussian input files

Mopac

• changepdb (/teo/bio/Bin)

Reads a pdb file and writes a Mopac input file

Mulliken

• changepdb (/teo/bio/Bin)

Reads a pdb file and writes a Mulliken input file

Pdb

• changeparm (/teo/bio/Bin)

Reads an Amber parameter file and writes out a pdb file
• changepdb (/teo/bio/Bin)

Reads and makes all types of modifications of a pdb file. Writes various output files.
• describe (/teo/bio/Bin)

Reads pdb, Turbomole, Gaussian, and Mulliken output files
Describes the geometry around an atom (typically a metal)
Describes hydrogen bonds in the system
Describe water interactions
Performs all types of analysis of Hessians (frequency analysis, force constants a la Seminario, CNS parameter and topology files).
• gausstopdb

Constructs a pdb file from the final Gaussian coordinates
• mimic (/teo/ulf/Bin)
  Constructs a pdb file (with correct format for metals) from a Turbomole file
• mtilt (/teo/ulf/Bin)

Calculates the tilt angle of a pdb file with standard atom names (of MMP)
• pdbtoamber

Reads a pdb file and sets up an Amber calculation (link, edit, parm files)
• pdbtocnsrefl

Converts a reflection file from pdb to CNS format
• pdbtocomqum
• turbotopdb
  Reads Turbomole data and writes out a pdb file (not MacMimic format)

 

Turbomole

• changemos

Reads Turbomole mos, alpha, beta, and natural files
Writes out dominant orbital components
Sets up a counter-poise calculation
Sets up a fragment calculation
Constructs starting orbitals to a Gaussian calculation
• changepdb (/teo/bio/Bin)

Reads a pdb file and writes a Turbomole input file
• comqumtoturbo
• describe (/teo/bio/Bin)

Reads pdb, Turbomole, Gaussian, and Mulliken output files
Describes the geometry around an atom (typically a metal)
Describes hydrogen bonds in the system
Describe water interactions
Performs all types of analysis of Hessians (frequency analysis, force constants a la Seminario, CNS parameter and topology files).
• espprep

Prepares a Turbomole calculation for calculations of ESP charges
• hesstofoa

Converts a Turbomole hessian ($hessian projected) to a force constant matrix ($forceapprox)
• jobexo

jobex with offset forces
• mimic (/teo/ulf/Bin)

Constructs a pdb file (with correct format for metals) from a Turbomole file
• mul

Sets up and runs a closed shell Mulliken analysis
• mul2

Sets up, runs, and postprocesses a open-shell Mulliken analysis. Gives charges and spin densities.
• readmul

Reads a Mulliken output file and concentrate the interesting result
• readmul2

Reads two Mulliken output files (from an open-shell calculation) and concentrate the interesting results (charges and spin densities)
• tfindmax

Finds the lowest energy in a Turbomole calculation
• tilt

Reads a Turbomole file and calculates the tilt angle of two planes
• turbotomolcas
  Reads Turbomole data and constructs Molcas or Gaussian input files
• turbotopdb
  Reads Turbomole data and writes out a pdb file (not MacMimic format)

 

Text

• purmail (/teo/ulf/Bin)

Removes unnecessary information from a mbox file.
Result in the file mbox.temp
• sumcol (/teo/ulf/Bin)

Calculates sum, min, max, and stdev of data in columns

Other

• dolink (/teo/bio/Bin)

Constructs links for fortran files
• makeintco

Constructs internal coordinates (from what?)