° | 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: 2024/10/04
° | 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: 2024/10/04
° | 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 protein on top of a monoelemental face-centerd cubic crystal metal surface as quickly as possible Written by: Elmar Krieger & Kornel Ozvoldik License: GNU GPL Last modified: 2024/10/04
° | Running a molecular dynamics simulation of a protein on top of a metal surface with normal or fast speed |
This macro sets up and runs a simulation of a protein on top of a monoelemental face-centerd cubic crystal metal surface Written by: Elmar Krieger & Kornel Ozvoldik License: GNU GPL Last modified: 2024/10/04
° | 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
° | 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
° | 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: 2023/05/08
° | 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
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