Gabedit with a generic program
You can now use your own program to compute energy, to optimize the geometry, to make an Molecular dynamic simulation or to search conformations via an MD simulation.
Gabedit create an input file for the external program, this program compute energy, dipole, gradients or optimize the geometry.
This program must produce an output file supported by Gabedit.
The input file for the external program (or script) create by gabedit contain :
First line is an integer : 0 for energy, 1 for gradients and 2 for optimization
Second line contains the text "Geometry"
Third line number of atoms, charge and multiplicity
From forth line, symbol, mmtype, pdftype, residuename, interger, charge, interger, integer, x y z (in Angstrom) and connectivities
Here is an example of an input file generated by gabedit:
2
Geometry
3 0 1
O OW OW HOH 0 -0.834000000000 2 1 0.000000000000 -0.388000011444 0.000000000000 2 2 1 3 1
H HW HW1 HOH 0 0.417000000000 2 1 0.750999987125 0.194000005722 0.000000000000 1 1 1
H HW HW2 HOH 0 0.417000000000 2 1 -0.750999987125 0.194000005722 0.000000000000 1 1 1
The external program must produce an output file with :
Energy in atomic unit in first line
Dipole in atomic unit in the second line
Gradients (atomic unit) in next lines if gradients are required (3 reals by line, for each atom)
Geometry in next lines if the geometry optimization is required.
Here is an example of an output file to generate by the external program and read by gabedit:
-4.077938
0.0 0.0 0.0
Geometry
3 0 1
O O O O 0 0.0 2 1 0.00000000 -0.38268179 0.00000000 0
H H H H 0 0.0 2 1 0.77848159 0.19134089 -0.00000000 0
H H H H 0 0.0 2 1 -0.77848159 0.19134089 0.00000000 0
As examples , see :
The script runDFTBPGabedit as an example
The script runGamessPM3 is another example.
To use this option, from the menu of the "Draw Window", select (Semi-)empirical/Generic energy, or Generic optimization or MD or MD conformations.
For MD, click on use generic program with command from "Model" page.