5. Additional Modules#
5.1. OUTIN#
Manipulation of input/output files
outin ⟨file_inp.ext⟩ ⟨file_out.ext⟩ [⟨-options⟩]
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FILE FORMATS [-ff]
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.ext: com : Gaussian (read/write)[gjf]
inp : ORCA (read/write)
xyz : xTB (read/write)
gro : GROMACS (read/write)
pdb : PDB (read/write)
log : Gaussian (read)
out : ORCA (read)
xtb : xTB (read)
xtc : GROMACS (read)
trj : XYZ/GRO/PDB (read)
+ ----------------------------------------------------------
cpt : Data Comp (write)[Compress calculated data]
dat : Calc Data (write)[Extract calculated data (option: nogeom)]
sup : Supl Data (write)[Extract supplementary data]
sep : Sepa Data (write)[Separate input/output data]
spl : Splt Data (write)[Split input/output data]
div : Divd Data (write)[Divide input/output data]
job : Jobs Exec (write)[Divide input/output jobs]
frq : Calc Frqs (write)[Extract vibrational frequency data]
ifr = Imag Dist (write)[Imaginary mode distortion (factor of distortion)]
+ ----------------------------------------------------------
slt : SLTs Extn (write)[Solute extraction from trajectory frames]
svt : SVTs Extn (write)[Solvent extraction from trajectory frames]
pcf = PChg File (write)[Solvent as discrete point charges]
-------------------------------------------------------------------------------------------------
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CONVERTION OPTIONS [-co]
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-key = “List of keywords” (for Gaussian or ORCA). [-kw]
-add = “List of keywords/additional” (for Gaussian). [-ad]
-svt = Include solvent type for implicit (with ALPB or PCM solvation method). [-sv]
-nmr : Include configuration for NMR calculation (for ORCA). [-nm]
+ ----------------------------------------------------------
-itr = Extract structure nº N of a trajectory. [Value: I] [-it](●)(■)
-ntr = Number N of equaly spaced MD steps for truncated trajectory. [Value: I] [-nt](●)(■)
-str = Extract equaly spaced frames at every M steps from trajectory. [Value: I] [-st] (■)
-ctr = Skipe I equilibration and extract J production MD steps (auto mode). [Value: [I:J]] [-ct](●)(■)
-btr = Select frames from I trajectory sections into J% final steps. [Value: [I:J]] [-bt] (■)
-ptr = Select frames aroud pressure P with tolerance ±D (in bar). [Value: [P:D]] [-pt] (■)
-nsm = Number of solvent molecules in the clustering process. [Value: I] [-ns](●)(■)
-bmc = Molal conc. of the microsolvation cluster (in mol·kg⁻¹). [Value: I] [-bc](●)(■)
-grp : Extract short-ranged non-bonded potential energies. [-gr] (■)
-nbx : Don´t make corrections for “fragmented” molecules near the box edges. [-nb] (■)
+ ----------------------------------------------------------
-prs = Include pressure configuration for thermodinamic calculation. [Value: N] [-pr]
-tmp = Include temperature configuration for thermodinamic calculation. [Value: N] [-tp]
-fcc = Final concentration after compression (in mol·L⁻¹). [Value: N] [-cf]
-frq = Scale factor for frequencies (for zero-point energy correction). [Value: N] [-sf]
-qha = Quasi-Harmonic Approximation (with optional cutoff frequency). [Value: <N>] [-fq]
-------------------------------------------------------------------------------------------------
(*) I,J = Integers; N,P,D = Real. (○) xTB available. (●) ORCA available. (■) GROMACS available.
5.2. SOLVS#
List of available solvents and ions for packaging
---------------------------------------------------- solvs [<solvent>] [<-option>] OPTIONS/DEFAULTS -field T [Force field parameters] ► ALL = All force fields ● OPL = OPLS-AA/L all-atom force field ○ LPG = OPLS-AA/L (from LigParGen) ○ QFC = OPLS-AA/L (from Q-Force) ● GRO = GROMOS96 54a7 force field ○ ATB = GROMOS96 54a7 (from ATB) ● CHM = CHARMM36 all-atom force field ● AMB = AMBER-GS force field ----------------------------------------------------
5.3. MDPAR#
List of available configuration files for MD simulations
--------------------------------------------------- mdpar [⟨-step N⟩] OPTIONS/DEFAULTS -step N [Step for extracting MDP parameters] ► 0/ALL = List all MDP files ○ 1/OPT = Box Optimization ○ 2/MIN = Energy Minimization ● 3/NVT = NVT Equilibration ● 4/NPT = NPT Equilibration ● 5/PRD = NPT Production ---------------------------------------------------
5.4. BONDS#
Hydrogen bonds analyzer
-------------------------------------------------------------------- bonds ⟨solute.ext⟩ ⟨solvent.ext⟩ [⟨-options⟩] PARAMETERS ⟨solute.ext⟩ [Input solute COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] ⟨solvent.ext⟩ [Input solvent COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] PROCEDURES -hbd [Use Solvate/HBONDS procedure (default)] [-hb] -crt B [Use xTB/CREST procedure with B% Boltzmann cutoff] [-cr] -dck N [Use ORCA/DOCKER procedure for N solvent molecules] [-dc] OPTIONS -xff [Use of GFN-FF method (faster determination)] [-xf] -xtb [Use of GFN2-xTB method (slower determination)] [-xt] -key [List of keywords for final optimization] [-kw] -svt T [Include explicit solvent and PCM configuration] [-sv] -prs M [Pressure for thermochemistry calculation (in atm)] [-ps] -tmp M [Temperature for thermochemistry calculation (in K)] [-tp] -con M [Final concentration after compression (in mol·L⁻¹)] [-fc] -prc P [Number of processors to be used] [-pc] -mem M [Amount of memory to use in GB] [-mm] -deb [Check generated inp file before submit] [-db] -for [Execute in forced mode] [-fm] -------------------------------------------------------------------- NOTE: This is an interface to CREST and ORCA programs.
5.5. CONFS#
Conformational analysis automator
-------------------------------------------------------------------- confs ⟨input.ext⟩ [⟨-options⟩] PARAMETERS input.ext [Input COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] OPTIONS -inp [Output file in ORCA format (default)] [-in] -gro [Output file in GROMACS format] [-gr] -pdb [Output file in PDB format (for LigParGen)] [-pd] -xyz [Output file in XYZ format (for LigParGen)] [-xy] -sep [Split the output file into its conformers] [-sp] -xff [Use GFN-FF in conformational analysis (default)] [-xf] -xtb [Use GFN2-xTB in conformational analysis (slower)] [-xt] -key [List of keywords for final optimization] [-kw] -svt T [Include implicity solvation configuration] [-sv] -prs M [Pressure for thermochemistry calculation (in atm)] [-ps] -tmp M [Temperature for thermochemistry calculation (in K)] [-tp] -con M [Final concentration after compression (in mol·L⁻¹)] [-fc] -prc N [Number of processors to be used] [-pc] -mem N [Amount of memory to use in GB] [-mm] -deb [Check generated inp file before submit] [-db] -for [Execute in forced mode] [-fm] -------------------------------------------------------------------- NOTE: This is an interface to CREST program.
5.6. CHECK#
Monitoring of procedures progress
-------------------------------------------------------------------- check ⟨input.ext⟩ [⟨compt.ext⟩] [⟨-options⟩] PARAMETERS input.ext [Input file] compt.ext [Compacted file] [Extensions: COM/INP/XYZ/LOG/OUT/XTB/TMP] OPTIONS -ext [Extract compacted internal file] (ex.: check inpfile.zip cptfile.cpt -ext) -del [Deletes compacted internal file][zip only] (ex.: check inpfile.zip cptfile.cpt -del) -ren [Renames compacted internal file][zip only] (ex.: check inpfile.zip oldfile.cpt -ren newfile.cpt) --------------------------------------------------------------------
5.7. CLEAN#
Cleaner for temporary files
5.8. COMPT#
Compression of output files
---------------------------------------- compt ⟨output.log/out/xtb⟩ [-chk] PARAMETERS output.ext [Output LOG/OUT/XTB file] ----------------------------------------
5.9. DEPLY#
Full deployment dependencies check
5.10. GCOPT#
gCalc SOC optmization procedure
----------------------------------------------------------------------------------------- gcopt ⟨slt.xyz/slt.slt/solute.gjf⟩ [⟨-options⟩] & PARAMETERS slt.xyz [Input XYZ/SLT/GJF file] OPTIONS/DEFAULTS -key K [List of keywords] [Default: "! M062X 6-31+G(d) Opt"] -svt A [Solvent type for CPCM solvation] [Default: None] -prs p [Pressure for thermochemistry (in bar)] [Default: 1.0] -tmp T [Temperature for thermochemistry (in K)][Default: 298.15] -cut N [Cut value for structural RMSD] [Default: 0.075] -opt [Perform a single geometry optimization][Default: Yes] -fgo [Perform a full geometry optimization] [Default: None] ADDITIONAL -prc P [Number of processors to be used] [Default: 4] -mem M [Amount of memory to use in GB] [Default: 8] -----------------------------------------------------------------------------------------
5.11. IMAGS#
Imaginary mode distortion
---------------------------------------- imags <output.log/out/xtb> [-img fator] PARAMETERS output.ext [Output LOG/OUT/XTB file] ----------------------------------------
5.12. INFOS#
Displaying system information
5.13. MOLAP#
Structural alignment for RMSD minimization
------------------------------------------------------------------------------------------- molap ⟨reference.ext⟩ ⟨structure.ext⟩ [⟨trajectory.trj.xyz⟩] [⟨-options⟩] PARAMETERS files.ext [Input COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] OPTIONS -bak [Save modified “structure” file with minimized RMSD (at system origin)] [-bk] -ref [Save modified “structure” file with minimized RMSD (at “reference” center)] [-rf] -str [Save modified “structure” file with minimized RMSD (at “structure” center)] [-st] -slt [Reorientation relative to the central solute fragment] [-sf] -------------------------------------------------------------------------------------------
5.14. RMSDS#
Calculation of structural RMSD and solute energy
------------------------------------------------------------------------------------ rmsds ⟨reference.ext⟩ ⟨structure.ext⟩ [⟨preoptimization.ext⟩] [⟨trajectory.trj.xyz⟩] PARAMETERS input.ext [Output COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] OPTIONS -min [Maximum structural superposition for RMSD minimization] [-mr] -bak [Save RMSD information in the input “structure” file] [-bk] -for [Force new calculation and override previous output] [-fm] ------------------------------------------------------------------------------------
5.15. SCALC#
Chemical shifts calculator
--------------------------------------------------------------------------- scalc ⟨input.trj.xyz⟩ [⟨-options⟩] PARAMETERS input.trj.xyz [Output TRJ file] OPTIONS -ato A [Atomic symbol of the species to be analyzed] [-at] -ref N [Reference value for chemical shifts (in ppm)] [-rf] -eqv [L] [List of equivalent atoms. (note: -eqv=[A1=A2:B1=B2=B3...])] [-eq] +----------------------------------------------------------+ -out F [Force reading specified ONIOM output file] [-of] -out [Force reading default ONIOM output file] [-of] +----------------------------------------------------------+ -hbd [Use BONDS data] [-hb] -gcc [Use GCALC data] [-gc] -plt [Plot the NMR spectrum] [-pt] --------------------------------------------------------------------------- * Note : Requires “gcc” file, and optionally “pcm” and “exp” files.
5.16. SOLVX#
Solvent identifier in clusters
------------------------------------ solvx ⟨file.trj.xyz⟩ PARAMETERS file.trj.xyz [Output TJR.XYZ file] ------------------------------------
5.17. STAND#
Modify input to standard orientation
------------------------------------------ stand ⟨input.ext⟩ & PARAMETERS input.ext [Input GJF/COM/INP/XYZ/GRO] ------------------------------------------
5.18. STATX#
Full statistical analysis directly from GMX program
--------------------------------- statx ⟨output.log⟩ PARAMETERS output.log [Output LOG file] ---------------------------------
5.19. SUBST#
Modification of texts in editable files
--------------------------------- subst ⟨input.ext⟩ "text1" "text2" PARAMETERS input.ext [Extensions: all] ---------------------------------
5.20. SUMMY#
Extraction of properties from output files
--------------------------------------------------------------------------------- summy ⟨output.log/out/xtb⟩ PARAMETERS output.ext [Output LOG/OUT/XTB file] OPTIONS/DEFAULTS -prs N [Pressure configuration for thermodinamic calculation] -tmp N [Temperature configuration for thermodinamic calculation] -fcc N [Final concentration after compression (in mol·L⁻¹)] -frq N [Scale factor for frequencies (for zero-point energy correction)] -qha <N> [Quasi-Harmonic Approximation (with optional cutoff frequency)] ---------------------------------------------------------------------------------
5.21. SUPPY#
Extraction of supplementary data from output files
--------------------------------------------------------------------------------- suppy ⟨output.log/out/xtb⟩ PARAMETERS output.ext [Output LOG/OUT/XTB file] OPTIONS/DEFAULTS -prs N [Pressure configuration for thermodinamic calculation] -tmp N [Temperature configuration for thermodinamic calculation] -fcc N [Final concentration after compression (in mol·L⁻¹)] -frq N [Scale factor for frequencies (for zero-point energy correction)] -qha <N> [Quasi-Harmonic Approximation (with optional cutoff frequency)] ---------------------------------------------------------------------------------
5.22. SVIEW#
Visualization of input/output files
-------------------------------------------------------------------------------- sview ⟨input.ext⟩ [⟨-options⟩] & PARAMETERS input.ext [Input file]⁽*⁾ GENERAL OPTIONS -try I [Generate a try file with N truncated steps (.trj file)] -vmd [Force file open with VMD program] -cpt [Perform compression of input/output files for GVW program] JMOL OPTIONS -noc [Run without input convertion] VMD OPTIONS -cpk [Show solute with VDW representation] -vdw [Show solute with VDW representation] -lico [Activate Licorice for solvent shell] -dyna [Activate DynamicBonds for solvent shell] -surf [Activate QuickSurf for solvent shell] -text [Execute in a text mode] -------------------------------------------------------------------------------- ⁽*⁾ Conversions: COM/GJF/LOG/INP/OUT/XYZ/XTB/PDB/GRO/TRJ
5.23. PDBIO#
PDB processor for Biomolecular systems
------------------------------------------------------------- pdbio ⟨input.pdb⟩ [⟨-options⟩] PARAMETERS input.pdb [Input PDB file] output.gro/itp [Output GRO/ITP file] OPTIONS/DEFAULTS -ffp T [Force field parameters] [Default: OPLS] * GRO = GROMOS96 54a7 force field * OPL = OPLS-AA/L all-atom force field ADDITIONAL -pdb [Archives PDB input] -gro [Generate GRO geometry file] -itp [Produces ITP forcefield file] -ion [Don't do ITP files of ionic species] -lap [Override PDB input file] -cls [Wipe all PDB comment lines] -bak [Create a backup of auxiliary files] -------------------------------------------------------------
5.24. PDB2X#
PDB cleaner module
-------------------------------- pdb2x ⟨input.pdb⟩ [⟨-options⟩] PARAMETERS input.pdb [Input PDB file] output.ent [Output ENT file] --------------------------------
5.25. IONIC#
PDB ions forcefield constructor
------------------------------------ ionic ⟨input.pdb⟩ [⟨-options⟩] PARAMETERS input.pdb [Input PDB file] output.gro/itp [Output GRO/ITP file] ------------------------------------
5.26. GROUT#
GRO files processor module
------------------------------------------------------------- grout ⟨input.gro/itp⟩ [⟨-options⟩] PARAMETERS input.gro/itp [Input GRO/ITP file] output.gro/itp [Output GRO/ITP file] OPTIONS -gro [Archives GRO input/output] -itp [Produces a concatenated ITP forcefield file] -pdb [Converts a PDB file to GRO input geometry] -------------------------------------------------------------
5.27. GRO2X#
GRO cleaner module
------------------------------------ gro2x ⟨input.gro/itp⟩ [⟨-options⟩] PARAMETERS input.gro/itp [Input GRO/ITP file] output.gro/itp [Output GRO/ITP file] ------------------------------------
5.28. GROTC#
GRO total charge calculator
------------------------------- grotc ⟨input.gro⟩ PARAMETERS input.gro [Input GRO file] -------------------------------
5.29. SUBMIT#
Run the program in the system queue
--------------------------------------------------- submit ⟨program⟩ ⟨input.ext⟩ ⟨-options⟩ ⟨-ntasks I⟩ PARAMETERS program [gsn/orca/xtb/gmx program] input.ext [Input GJF/COM/INP/XYZ/GRO file] OPTIONS/DEFAULTS -options [Program specific options] -queue T [Name of available queue] -ntasks I [Number of processors] [-prc] -qmemor I [Amount of memory (in GB)][-mem] -preserve [Preserve the submission job file] -debug [Check generated job before submit] AVAILABLE SYSTEM BATCH »Local Machine WARNING This is an open-source script that may require adjustments depending on the available queue system ---------------------------------------------------
5.30. runGSN#
Gaussian program interface
5.31. runGVW#
GaussView program interface
5.32. runORCA#
ORCA program interface
5.33. runXTB#
xTB program interface
5.34. runCREST#
CREST program interface
5.35. runGMX#
GROMACS program interface
5.36. runBABEL#
oBabel program interface
5.37. runJMOL#
JMol program interface
5.38. runVMD#
VMD program interface
5.39. runPACKMOL#
PackMol program interface
5.40. runQFORCE#
Q-Force program interface