Comprehensive Contents Page - Revision history

Nn320: /* PATHSAMPLE */

2021-10-28T10:17:15Z

PATHSAMPLE

← Older revision		Revision as of 10:17, 28 October 2021
Line 148:		Line 148:
	* [[Biomolecules in PATHSAMPLE]]		* [[Biomolecules in PATHSAMPLE]]
	* [[Biomolecules in the energy landscape framework]]		* [[Biomolecules in the energy landscape framework]]
			* [[Adding several minima obtained using GMIN (maybe using BHPT) to min.data]]
	* [[Expanding the kinetic transition network with PATHSAMPLE]]		* [[Expanding the kinetic transition network with PATHSAMPLE]]
	* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]		* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]

2021-10-07T16:01:36Z

AMBER

← Older revision		Revision as of 16:01, 7 October 2021
Line 178:		Line 178:
	* [[Simple scripts for LEaP to create topology and coordinate files]]		* [[Simple scripts for LEaP to create topology and coordinate files]]
	* [[Preparing an AMBER topology file for a protein system]] - step by step guide		* [[Preparing an AMBER topology file for a protein system]] - step by step guide
			* [[Preparing input files for a peptide using AMBER]] - detailed guide
	* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system		* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
	* [[Using Molfacture to edit molecules and add hydrogens]]		* [[Using Molfacture to edit molecules and add hydrogens]]

2021-07-01T11:40:16Z

DISCOTRESS

← Older revision		Revision as of 11:40, 1 July 2021
Line 164:		Line 164:
	=== [[Quasi-continuous interpolation for biomolecules \| QCI]] ===		=== [[Quasi-continuous interpolation for biomolecules \| QCI]] ===

	=== [[Detailed kinetic network analysis with ~~DISCOTRESS \|~~ DISCOTRESS]] ===		=== [[DISCOTRESS \| Detailed kinetic network analysis with DISCOTRESS]] ===

	== Non-Group Software ==		== Non-Group Software ==

2021-07-01T11:39:45Z

Useful Notes on Wales Group Programs and Subroutines

← Older revision		Revision as of 11:39, 1 July 2021
Line 163:		Line 163:

	=== [[Quasi-continuous interpolation for biomolecules \| QCI]] ===		=== [[Quasi-continuous interpolation for biomolecules \| QCI]] ===

			=== [[Detailed kinetic network analysis with DISCOTRESS \| DISCOTRESS]] ===

	== Non-Group Software ==		== Non-Group Software ==

2021-07-01T11:35:33Z

Programs

← Older revision		Revision as of 11:35, 1 July 2021
Line 40:		Line 40:
	* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.		* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
	* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.		* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.
			* [[DISCOTRESS]]: A program to perform detailed quantitative analysis of a kinetic network (stationary point database)

	=== Curated Examples ===		=== Curated Examples ===

2020-09-28T10:09:54Z

Acquiring and compiling the group software: Link to Git page

← Older revision		Revision as of 10:09, 28 September 2020
Line 6:		Line 6:
	=== Acquiring and compiling the group software ===		=== Acquiring and compiling the group software ===
	* [[SVN setup]]		* [[SVN setup]]
			* [[Git Workflow]]
	* [[Wales Group Version control]] - to keep the code standardised.		* [[Wales Group Version control]] - to keep the code standardised.
	* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.		* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.

2020-07-10T23:45:13Z

PATHSAMPLE

← Older revision		Revision as of 23:45, 10 July 2020
Line 156:		Line 156:
	* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.		* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
	* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE		* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
			* [[STARTING INITIAL PATH JOBS WITH PATHSAMPLE]]: How to start initial path jobs with PATHSAMPLE if no min.data or path.info files are present.

	=== [[Notes on MINPERMDIST \| MINPERMDIST]] ===		=== [[Notes on MINPERMDIST \| MINPERMDIST]] ===

2020-06-03T10:12:13Z

AMBER

← Older revision		Revision as of 10:12, 3 June 2020
Line 183:		Line 183:
	* [[Mutational BH steps]]		* [[Mutational BH steps]]
	* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.		* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
			* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
	* [[REMD with AMBER]]		* [[REMD with AMBER]]
	* [[Performing a hydrogen-bond analysis]]		* [[Performing a hydrogen-bond analysis]]

2020-06-03T10:11:38Z

PATHSAMPLE

← Older revision		Revision as of 10:11, 3 June 2020
Line 155:		Line 155:
	* [[Connecting Sub-databases]]		* [[Connecting Sub-databases]]
	* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.		* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
			* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE

	=== [[Notes on MINPERMDIST \| MINPERMDIST]] ===		=== [[Notes on MINPERMDIST \| MINPERMDIST]] ===

2020-06-02T16:21:20Z

AMBER

← Older revision		Revision as of 16:21, 2 June 2020
Line 181:		Line 181:
	* [[Evaluating different components of AMBER energy function with SANDER]]		* [[Evaluating different components of AMBER energy function with SANDER]]
	* [[Mutational BH steps]]		* [[Mutational BH steps]]
			* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
	* [[REMD with AMBER]]		* [[REMD with AMBER]]
	* [[Performing a hydrogen-bond analysis]]		* [[Performing a hydrogen-bond analysis]]