From e273c0c599ae73d803e8b89c4ff2a2d645a66f64 Mon Sep 17 00:00:00 2001 From: Noora Azadvari Date: Fri, 3 May 2024 18:31:33 -0400 Subject: [PATCH 1/3] Scoring using weights (*.wts) files --- ...GAMESSEnergyCalculationFromWeigthsFiles.md | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md diff --git a/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md new file mode 100644 index 000000000..b5e8a1ef7 --- /dev/null +++ b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md @@ -0,0 +1,32 @@ +[ This page is temporary to avoid conflicts on branches. The content will be moved to single point scoring with gamess] + +## + +There are different ways to set a scoring function. One can also use a weights file for this purpose. You will need to create a file with `.wts` format in directory `to be written`. Here is an example of content in this file: + +``` +BEGIN_GAMESS_SETTINGS +gamess_threads="2" +gamess_basis_set="N31" +gamess_ngaussian="4" +gamess_dft_functional="B3LYPV3" +gamess_electron_correlation_treatment="DFT" +gamess_max_scf_iterations="100" +gamess_fmo_calculation="true" +gamess_max_fmo_monomer_scf_iterations="100" +gamess_hybrid_molecular_orbital="4-31G" +gamess_hybrid_molecular_orbital_file="tools/fmo/HMO/c.txt" +END_GAMESS_SETTINGS + +BEGIN_GAMESS_QM_CONFIGURATION +fmo_fragmentation_method="carbon_carbon_favouring_residue_based_fragments" +END_GAMESS_QM_CONFIGURATION + +gamess_qm_energy 1.0 +``` + +In the first block, `BEGIN_GAMESS_SETTINGS ... END_GAMESS_SETTINGS` you can use any tag that is used in `` section in Rosetta scripts. + +In the second block, `BEGIN_GAMESS_QM_CONFIGURATION ... END_GAMESS_QM_CONFIGURATION` you can list all setting related to gamess configurations. (similar to what in scripts??) + +The last section `gamess_qm_energy 1.0` set a weight of `1.0` for `gamess_qm_energy` score term. This number will be multiplied by the output of `gamess_qm_energy` to give a final score. Therefore, setting it to `1.0` will give the original score. One might change it to change the scale of score for different reasons. Note that the output of RosettaQM has a unit of **kcal/mol**. \ No newline at end of file From 22e220fa69eb89b2517fe613ded52139c1c45e8e Mon Sep 17 00:00:00 2001 From: Noora Azadvari Date: Mon, 6 May 2024 16:25:51 -0400 Subject: [PATCH 2/3] updating configuration part --- .../RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md index b5e8a1ef7..eb8849c79 100644 --- a/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md +++ b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md @@ -27,6 +27,6 @@ gamess_qm_energy 1.0 In the first block, `BEGIN_GAMESS_SETTINGS ... END_GAMESS_SETTINGS` you can use any tag that is used in `` section in Rosetta scripts. -In the second block, `BEGIN_GAMESS_QM_CONFIGURATION ... END_GAMESS_QM_CONFIGURATION` you can list all setting related to gamess configurations. (similar to what in scripts??) +In the second block, `BEGIN_GAMESS_QM_CONFIGURATION ... END_GAMESS_QM_CONFIGURATION` you can use any tag that is used in `` section in Rosetta scripts. The last section `gamess_qm_energy 1.0` set a weight of `1.0` for `gamess_qm_energy` score term. This number will be multiplied by the output of `gamess_qm_energy` to give a final score. Therefore, setting it to `1.0` will give the original score. One might change it to change the scale of score for different reasons. Note that the output of RosettaQM has a unit of **kcal/mol**. \ No newline at end of file From 100cd8b1eb14bdddf0d7bcc034c9c8202c9dfa49 Mon Sep 17 00:00:00 2001 From: Noora Azadvari Date: Mon, 6 May 2024 16:29:19 -0400 Subject: [PATCH 3/3] weights path --- .../RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md index eb8849c79..f8a2e9166 100644 --- a/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md +++ b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSEnergyCalculationFromWeigthsFiles.md @@ -2,7 +2,7 @@ ## -There are different ways to set a scoring function. One can also use a weights file for this purpose. You will need to create a file with `.wts` format in directory `to be written`. Here is an example of content in this file: +There are different ways to set a scoring function. One can also use a weights file for this purpose. You will need to create a file with `.wts` format in directory `/main/database/scoring/weights`. Here is an example of content in this file: ``` BEGIN_GAMESS_SETTINGS