YASARA menu YASARA menu

° 

Molecular dynamics

° 

Movies

To install a movie, just download the ZIP file and unpack it in the yasara/mov directory (which of course requires that you have at least YASARA View installed). MacOS tries to hide the yasara directory from you: open Finder, browse to the YASARA application and click on 'Show package contents' in the context menu to see the yasara directory.

If you then click on Help > Play help movie, the new movie will appear in the list.

Movies are simply YASARA macros that use multimedia elements to create interactive tutorials or presentations. Works well instead of the usual PowerPoint approach. Instructions how to create your own movies can be found in the YASARA documentation by clicking on 'Recipes - Answer complex questions' -> 'Create your own YASARA movies'.

° 

Virtual reality simulations (PC)

Figure: A snapshot from the movie
A tutorial explaining how to work with MD simulations in VR

Written by: Kornel Ozvoldik, Elmar Krieger, Elina Krieger

License: GNU GPL

Last modified: 2023/08/21

Download: vrintro3.zip

° 

Simulation and quantum mechanics of small molecules

Figure: A snapshot from the movie
This tutorial introduces fractional bond orders and pH dependency, shows how to build and simulate small molecules, and how to use quantum mechanics to optimize geometries and compare tautomers.

Written by: Elmar Krieger

License: GNU GPL, except coral reef background by Ove Hoegh-Guldberg (Centre for Marine Studies, University of Queensland)

Last modified: 2023/02/22

Download: smallmol2.zip

° 

Accurate simulations in water

Figure: A snapshot from the movie
Written by: Elmar Krieger

License: GNU GPL

Last modified: 2020/05/12

Download: mdwater.zip

° 

Simulation in dodecahedral cells

Figure: A snapshot from the movie
A tutorial explaining how dodecahedral simulation cells work.

Written by: Kornel Ozvoldik

License: GNU GPL

Last modified: 2020/05/09

Download: mdcell.zip

° 

The YAMBER force field, ICMSB 2003

Figure: A snapshot from the movie
Written by: Elmar Krieger

License: GNU GPL

Last modified: 2020/05/09

Download: yamber.zip

° 

The theory behind molecular dynamics simulations

Figure: A snapshot from the movie
Written by: Elmar Krieger

License: GNU GPL

Last modified: 2020/05/09

Download: mdintro.zip

° 

Interactive simulations for modeling

Figure: A snapshot from the movie
Written by: Elmar Krieger

License: GNU GPL

Last modified: 2020/05/06

Download: mdinteract.zip

° 

Plugins

Plugins are Python scripts or Yanaconda macros that extend YASARA's user interface and get activated when you click the respective option. They are the method of choice to extend YASARA with your own functions.

All plugins are distributed together with YASARA and should be available from the graphical user interface. Windows users need to have Python from www.python.org installed.

To reinstall a plugin, just download the ZIP file and unpack it in the yasara/plg directory. If you then restart YASARA, the new options will appear in the menus. If you are not sure where the option appears, look at the top of the main plugin file (*.mcr or *.py).

° 

Sample cartesian space with CONCOORD

This plugin runs the CONCOORD program and creates an ensemble of structures that span the conformational space of the selected protein, click Edit > Sample > Object. Requires YASARA Version 4.3.13. Currently only Linux is supported. More information about CONCOORD can be found at http://www.mpibpc.gwdg.de/abteilungen/071/bgroot/concoord.html. CONCOORD is automatically downloaded from this site the first time you use the plugin. Please cite: B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend and H.J.C. Berendsen; "Prediction of protein conformational freedom from distance constraints", Proteins 29: 240-251 (1997). If the structure contains lots of bumps, this may cause convergence problems, so it is best to use only energy minimized structures.

Written by: Bert de Groot

License: GNU GPL

Last modified: 2017/04/15

Download: concoord.zip

° 

Color atoms by force acting on them

This plugin colors all atoms by the force acting on them. This is helpful to identify regions of conformational stress. Blue means zero force (<1000 pN), red medium force and yellow maximum force (>5000 pN). Click View > Color > All by force.

Written by: Sander Nabuurs

License: GNU GPL

Last modified: 2014/03/20

Download: colorforce.zip

° 

Macros

Macros are written using the Yanaconda language. If you already know a programming language, you can learn Yanaconda in 15 minutes, otherwise it may take 30.

To install, just save the macro in the directory yasara/mcr or wherever you want it. The syntax of Yanaconda is described in the YASARA documentation.

° 

Analyzing the ligand binding energy during a molecular dynamics simulation

This macro calculates the binding energy of a ligand during a molecular dynamics simulation, including the time average. If you didn't use AMBER14 for the MD, adapt the ForceField setting below for consistency. By default, the receptor must be object 1, the ligand must be object 2 (or change the settings). More positive energies indicate better binding, negative energies DO NOT indicate no binding, see the 'BindEnergy' command in the user manual for details, also for words of caution, a much more sophisticated approach is in preparation.

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2024/12/10

° 

Convert between Sim, XTC, MDCrd and PDB simulation trajectories

This macro converts an existing MD trajectory between various formats. Supported are conversions between YASARA Sim, GROMACS XTC and AMBER MDCrd trajectories, as well as conversion to PDB files

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2024/11/28

Download: md_convert.mcr

° 

Running a molecular dynamics simulation of a protein on top of a metal surface with maximum speed

This macro sets up and runs a simulation of a molecule's adsorption on a face-centered cubic metal surface

Written by: Elmar Krieger & Kornel Ozvoldik

License: GNU GPL

Last modified: 2024/10/05

° 

Running a molecular dynamics simulation of an adsorbate on a metal surface with normal or fast speed

This macro sets up and runs a simulation of a molecule's adsorption on a face-centered cubic metal surface

Written by: Elmar Krieger & Kornel Ozvoldik

License: GNU GPL

Last modified: 2024/10/05

° 

Analyzing a molecular dynamics trajectory

This macro analyzes a simulation and creates a detailed report with a large number of plots, e.g. energies, RMSDs, hydrogen bonds. It also tries to identify the main ligand and provides ligand-specific data. All results are additionally written to a simple text table, which can be imported into your favorite spreadsheet program. Your own analysis can often be added with just one line of code, search for 'Example:'.

Written by: Elmar Krieger and Kornel Ozvoldik

License: GNU GPL

Last modified: 2024/10/05

Download: md_analyze.mcr

° 

Running the DHFR benchmark to measure MD performance

This macro runs the DHFR benchmark for about 10 seconds and displays the results

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2024/09/10

° 

Running a molecular dynamics simulation of a membrane protein with normal or fast speed

This macro sets up and runs a simulation of a membrane protein. It scans the protein for secondary structure elements with hydrophobic surface residues, orients it accordingly and embeds it in a membrane of adjustable lipid composition. Finally a 250 ps restrained equilibration simulation is run, which ensures that the membrane can adapt to the newly embedded protein. Then the real simulation starts.

Written by: Elmar Krieger & Kornel Ozvoldik

License: GNU GPL

Last modified: 2024/05/14

° 

Running a steered molecular dynamics simulation in water

This macro sets up and runs a steered simulation to pull a ligand from its binding site. As soon as they have been pulled apart completely and atoms start crossing periodic boundaries, the macro works no longer correctly. You can set the pulling 'acceleration' below, which is not changed during the simulation. So this macro can currently not tell you how strong you need to pull, it can only tell you whether the chosen acceleration is strong enough or not to pull the ligand off.

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2023/10/16

° 

Play back a molecular dynamics trajectory

This macro provides an interactive molecular dynamics trajectory player

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2023/10/16

Download: md_play.mcr

° 

Analyzing a molecular dynamics trajectory in blocks

This macro analyzes a simulation in blocks. YASARA runs for each block the md_analyze macro and creates in the end a single report containing detailed information about the system, e.g. energies, RMSDs, hydrogen bonds per block. By default the simulation snapshots are split into 3 blocks, so the second and third block can be compared to see if convergence has been reached. The number of blocks can be freely choosen as well as setting the number of snapshots to be compiled into one block instead. For more information about the methods used and how to add your own analysis see the md_analyze macro.

Written by: Elmar Krieger and Kornel Ozvoldik

License: GNU GPL

Last modified: 2023/10/16

° 

Refining a homology model by molecular dynamics simulation in water

This macro runs a 500 ps simulation of a homology model using the protocol described in Proteins 57,678-683. It saves one PDB file every 25 picoseconds, including a table with force field energies to identify the best snapshot. In YASARA Structure, this table additionally contains Dihedrals, Packing1D and Packing3D checks (see the Check command). And in the Twinset, three more checks are included: PhiPsi, Backbone and Packing3. Note that MD simulations tend to make models worse if you simulate too long.

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2023/05/08

Download: md_refine.mcr

° 

Analyzing the change of secondary structure in a molecular dynamics trajectory

This macro analyzes a simulation and creates a table with per-residue secondary structure as well as a graphical plot (save a ray-traced screenshot with 'Ball zoom' set to 2).

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2023/05/08

° 

Analyzing a molecular dynamics trajectory per residue

This macro analyzes a simulation and creates a table with average RMSFs and RMSDs from the starting structure per residue

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2023/05/08

° 

Analyzing a molecular dynamics trajectory of multiple objects

This macro analyzes a simulation and creates a table with energies and RMSDs from the starting structures for multiple objects

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2023/05/08

° 

Running a molecular dynamics simulation of a membrane protein with maximum speed

This macro sets up and runs a simulation of a membrane protein as quickly as possible. It scans the protein for secondary structure elements with hydrophobic surface residues, orients it accordingly and embeds it in a membrane of adjustable lipid composition. Finally a 250 ps restrained equilibration simulation is run, which ensures that the membrane can adapt to the newly embedded protein. Then the real simulation starts.

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2020/11/10

° 

Running an accurate molecular dynamics simulation in water with maximum speed

This macro runs a simulation as quickly as possible, using the standard macro md_run.

Written by: Elmar Krieger

License: GNU GPL

Last modified: 2015/03/24

Download: md_runfast.mcr