Macromodel to gaussian: Difference between revisions
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go back to [[Main Page]], [[Computational Resources]], [[Scripts]] | go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[Scripts for Gaussian]] | ||
These are a group of AWK and | These are a group of AWK and bash/cshell scripts to chose the conformers of the Macromodel search, cut their geometries,prepare new inputs and send it to the queue. | ||
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2.- Chose which of the conformers found by Macromodel would you like to compute by using Gaussian. To do so, look at the energies and geometries. Use the script [[confliste]] to get a list of the number of conformer and the energy. | 2.- Chose which of the conformers found by Macromodel would you like to compute by using Gaussian. To do so, look at the energies and geometries. Use the script [[confliste]] to get a list of the number of conformer and the energy. | ||
confliste name-out.mae > list | confliste name-out.mae > list | ||
the file list will contain all the isomers and energies | the file list will contain all the isomers and energies. '''Edit the list''' file and remove all the isomers you don't want to optimize with Gaussian. The first isomer (1 0.00), does not appear on the list, but the input will be automatically generated. | ||
4.- Prepare 2 files called part1 and part2 with the beginning (command line, title, charge & multiplicity) and the end (basis sets, pseudos & other) for your new Gaussian input files. Look at the following examples: [[part1]], [[part2]]. Save them in the same directory as your name-out.mae | |||
5.- Execute the program by typing | |||
makeconf name-out | makeconf name-out | ||
The files name-out_confX.in will be sent to the queue, if you don't want them to be sent directly to the queue delete the qs 1 q g03 lines in the makeconf script. | The files name-out_confX.in will be sent to the queue, if you don't want them to be sent directly to the queue delete the qs 1 q g03 lines in the makeconf script. | ||
! If you have used a different type of atom in the Macromodel search than the one you want to use in the Gaussian calculation, you have 2 possibilities:1) add a line in the makeconf with sed s/XX/YY/g or 2) edit the name-out.mae prior to execute the makeconf, and change the type of atom in column 21 of the first set of coordinates. | ! If you have used a different type of atom in the Macromodel search than the one you want to use in the Gaussian calculation, you have 2 possibilities: 1) add a line in the makeconf with "sed s/XX/YY/g" or 2) edit the name-out.mae prior to execute the makeconf, and change the type of atom in column 21 of the first set of coordinates. | ||
! You may need to adjust the number of ":::" between the energy of the conformer and the coordinates, in the file "conf" according to your output. | |||
Latest revision as of 13:26, 13 September 2011
go back to Main Page, Computational Resources, Scripts, Scripts for Gaussian
These are a group of AWK and bash/cshell scripts to chose the conformers of the Macromodel search, cut their geometries,prepare new inputs and send it to the queue.
To proceed you need to follow the subsequent steps:
1.- Copy the scripts: confliste, conf and makeconf to you directory /home/username/bin/.
2.- Chose which of the conformers found by Macromodel would you like to compute by using Gaussian. To do so, look at the energies and geometries. Use the script confliste to get a list of the number of conformer and the energy.
confliste name-out.mae > list
the file list will contain all the isomers and energies. Edit the list file and remove all the isomers you don't want to optimize with Gaussian. The first isomer (1 0.00), does not appear on the list, but the input will be automatically generated.
4.- Prepare 2 files called part1 and part2 with the beginning (command line, title, charge & multiplicity) and the end (basis sets, pseudos & other) for your new Gaussian input files. Look at the following examples: part1, part2. Save them in the same directory as your name-out.mae
5.- Execute the program by typing
makeconf name-out
The files name-out_confX.in will be sent to the queue, if you don't want them to be sent directly to the queue delete the qs 1 q g03 lines in the makeconf script.
! If you have used a different type of atom in the Macromodel search than the one you want to use in the Gaussian calculation, you have 2 possibilities: 1) add a line in the makeconf with "sed s/XX/YY/g" or 2) edit the name-out.mae prior to execute the makeconf, and change the type of atom in column 21 of the first set of coordinates.
! You may need to adjust the number of ":::" between the energy of the conformer and the coordinates, in the file "conf" according to your output.