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ONIOM tips:
ONIOM tips:
* REMEMBER; all ONIOM calculations should contain the connectivity and the atom types correctly set up (as in MM calculations). And should be the same for all species you wish to compare


* You can use iop(4/33=2) to print out all MM contributions.
* You can use iop(4/33=2) to print out all MM contributions.
* To get out the model system from an oniom calculation include iop(1/33=2). In the output file, search for: "ONIOM: generating point 2 high level on model system". All atoms without the label -1 belong to the model system (this list includes also the link hydrogens).
* To get out the model system from an oniom calculation include iop(1/33=2). In the output file, search for: "ONIOM: generating point 2 high level on model system". All atoms without the label -1 belong to the model system (this list includes also the link hydrogens).
* There are two options if you want to check other force fields which are not implemented in Gaussian09;


Option1: You can do one-dimensional potential energy surface scans over a reaction coordinate, where the constrained structure optimisations at the potential energy surface can be performed with ONIOM(DFT:UFF), ONIOM(DFT:DREIDING) or ONIOM (DFT:AMBER), where the iop(1/33=2) option helps to obtain QM and MM parts of the molecule. Then you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER, where they have various force filed parameters.
* [[Force Fields not implemented]] To use force fields which are not implemented in Gaussian09, you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER.


Option2: ´External´ keyword.
* In Gaussview: When selecting MM regions in QM/MM methods you can change the status (H/L) of several atoms at same time, by:i) select the upper atom in the list ii) go to the last one and press control+shift 3) change the last atom status to low level.


There are two examples in the G09 test suite which make use of the ´External´ keyword.  
* GaussView can help assigning atom types and it will also add point charges according to the AMBER convention for atoms in standard protein residues. For other molecules that are not standard residues, there is no information about appropriate charges (GaussView will try to assign reasonable atom types), so one would need to derive charges for the atoms in such molecule, or look in the literature to see if other researchers have derived charges and parameters for such molecule.


(1) Test726 uses a shell script to run g09 as an external process with UFF. The script ´extuffex´ is stored in the g09/bsd directory.
* Only the "amber96" version is internally hardwired in the G09 code and that is the one selected when using the AMBER keyword. The "amber.prm" file in the "g09" directory is simply a text file that shows this same parameter file that is internally hardwired in the code, but the program does not read that file. It is included for illustrative purposes so one see examples of how to specify MM parameters manually. The files that you mentioned (amber98.prm and oplsaa.prm) unfortunately are not ready to be used. You can make modifications to the internally hardwired parameter file by adding the modifications to the input file, for instance: [[example_amber96]] If you do not want for G09 to use the internally hardwired parameter file but to read the full parameter table from an external file, you can do so with the "SoftOnly" option, which takes only the MM parameter specifications given in the input file and nothing from the internally hardwired parameter file. [[example_amber96soft]]


(2) Test769 uses a perl script, mygau, which is stored in the g09/bsd subdirectory. Note that you will likely need to edit mygau to change the path to perl, rather than /usr/local/bin, because most machines store it in /usr/bin.
* Partial charges for AMBER and ONIOM calculations can be generated in a couple of different ways.
1) For known AMBER residues, GaussView will generate the standard charges and supply them in the input file.


In both cases you could use ´External´ keyword in the input file.
2) For non-standard AMBER residues no charge will be generated but you can use AMBER=QEq and use the charge equilibration method of Rappe and Goddard developed for UFF.
 
Eg:-
ONIOM(B3LYP/6-31G(d):AM1:External="Script_name") Opt
 
How to use external MM program:
 
This is not fully implemented in G09. The Gau_External script in the G09 home is an example where we use Gaussian as an external program, specifically 'Gau_External' script helps to run MOPAC as external procedure for ONIOM. You would need to make a copy of this script and modify it to create an input file for other MM programes (Eg. TINKER), and run the MM program with this input, and then use the output from the MM program to generate result files suitable for processing by Gaussian.
 
 
* In Gaussview: When selecting MM regions in QM/MM methods you can change the status (H/L) of several atoms at same time, by:i) select the upper atom in the list ii) go to the last one and press control+shift 3) change the last atom status to low level.
* GaussView can help assigning atom types and it will also add point charges according to the AMBER convention for atoms in standard protein residues. For other molecules that are not standard residues, there is no information about appropriate charges (GaussView will try to assign reasonable atom types), so one would need to derive charges for the atoms in such molecule, or look in the literature to see if other researchers have derived charges and parameters for such molecule.
* Only the "amber96" version is internally hardwired in the G09 code and that is the one selected when using the AMBER keyword. The "amber.prm" file in the "g09" directory is simply a text file that shows this same parameter file that is internally hardwired in the code, but the program does not read that file. It is included for illustrative purposes so one see examples of how to specify MM parameters manually. The files that you mentioned (amber98.prm and oplsaa.prm) unfortunately are not ready to be used.


You can make modifications to the internally hardwired parameter file by adding the modifications to the input file, for instance:
3) You can generate charges from a single point calculation with Pop=MK. For example LSDA/3-21G or HF/6-31G(d) depending on the size of your system. Then get charges either from the Mulliken analysis or the electrostatic potential fitting. You will need to supply these manually in the input.

Latest revision as of 09:58, 29 July 2011

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ONIOM tips:

  • REMEMBER; all ONIOM calculations should contain the connectivity and the atom types correctly set up (as in MM calculations). And should be the same for all species you wish to compare
  • You can use iop(4/33=2) to print out all MM contributions.
  • To get out the model system from an oniom calculation include iop(1/33=2). In the output file, search for: "ONIOM: generating point 2 high level on model system". All atoms without the label -1 belong to the model system (this list includes also the link hydrogens).
  • Force Fields not implemented To use force fields which are not implemented in Gaussian09, you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER.
  • In Gaussview: When selecting MM regions in QM/MM methods you can change the status (H/L) of several atoms at same time, by:i) select the upper atom in the list ii) go to the last one and press control+shift 3) change the last atom status to low level.
  • GaussView can help assigning atom types and it will also add point charges according to the AMBER convention for atoms in standard protein residues. For other molecules that are not standard residues, there is no information about appropriate charges (GaussView will try to assign reasonable atom types), so one would need to derive charges for the atoms in such molecule, or look in the literature to see if other researchers have derived charges and parameters for such molecule.
  • Only the "amber96" version is internally hardwired in the G09 code and that is the one selected when using the AMBER keyword. The "amber.prm" file in the "g09" directory is simply a text file that shows this same parameter file that is internally hardwired in the code, but the program does not read that file. It is included for illustrative purposes so one see examples of how to specify MM parameters manually. The files that you mentioned (amber98.prm and oplsaa.prm) unfortunately are not ready to be used. You can make modifications to the internally hardwired parameter file by adding the modifications to the input file, for instance: example_amber96 If you do not want for G09 to use the internally hardwired parameter file but to read the full parameter table from an external file, you can do so with the "SoftOnly" option, which takes only the MM parameter specifications given in the input file and nothing from the internally hardwired parameter file. example_amber96soft
  • Partial charges for AMBER and ONIOM calculations can be generated in a couple of different ways.

1) For known AMBER residues, GaussView will generate the standard charges and supply them in the input file.

2) For non-standard AMBER residues no charge will be generated but you can use AMBER=QEq and use the charge equilibration method of Rappe and Goddard developed for UFF.

3) You can generate charges from a single point calculation with Pop=MK. For example LSDA/3-21G or HF/6-31G(d) depending on the size of your system. Then get charges either from the Mulliken analysis or the electrostatic potential fitting. You will need to supply these manually in the input.

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