oniomANALYSIS is a TCL script that allows an easy way to change the frozen status of each atom in Gaussian Hybrid Systems (ONIOM).

How to use?

Insert follow command in shell:

tclsh oniomFROZEN.tcl [A] [B] [C]

Where:

[A] is a flag which defines what type of job is going to be perfomed:

–readfile : residues of file \[C\] will be unfrozen and all others will be frozen

–frozenall : all atoms will be frozen

–unfrozenall : all atoms will be unfrozen

–invert : all previous unfrozen atoms will be frozen and all previous frozen atoms will be unfrozen

–invertnowater : equal to previous but all water molecules \(ResName=WAT\) will be frozen

[B] is the Gaussian 09 input file (.com)

[C] is a file with a list of residues (one number per line) to become unfrozen, frozen all other residues. ONLY works with the –readfile flag.

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oniomANALYSIS is a TCL script that allows an easy way to extract data and handling output files from Gaussian 09 calculations.

The script allows get informations about energy about low a high levels in hybrid systems (ONIOM). In this option, scripts generates two files:

• Energy of all structures
• Energy of all optimized structures

oniomANALYIS allows also extract the first and last structures and write them in a new input Gaussian files in order to run a following calculation recurring to a previous calculation. In this case two files will be generated:

• Gaussian input file of first structure
• Gaussian input file of last structure

Moreover, you could also extract PDB files from Gaussian output files:

• PDB file with all structures
• PDB file with all optimized structures
• PDB file with last structure
• PDB file with last optimized structure

How to use?

Insert follow command in shell:

tclsh oniomANALYSIS.tcl [A] [B]

Where:

[A] is a flag which defines what type of job is going to be perfomed:

–energy : for energy extraction

–gaussian : for Gaussian input files generation

–pdb : for PDB files generation

[B] is the Gaussian 09 output file (.log)

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