6.13. menu¶
It is a menu related to Amber.
Since Winmostar runs Amber on the Cygwin environment, in order to use this function, you need to set up CygwinWM is required.
6.13.1. Configure LEaP¶
Use tLEaP to set conditions for creating coordinate (crd) and topology (prmtop) files. Select each item, specify it, and click the [OK] button.
- Force Field
- Select the type of force field.
- Add Na +
- Specify whether to add Na ion, and specify the number.
- Add Cl-
- Specify whether to add Cl ions and specify the number.
- Solvate
- Specify whether to add water molecules.
- Box/Octahedron
- Specify the box type.
- Solvent
- Specify the type of solvent.
- Distance
- Specify the distance between the solute and the box boundary.
- Other LEaP Commands
- Write other LEaP commands.
6.13.2. Run LEaP¶
Create coordinates (crd) file and topology (prmtop) file using tLEaP. (Crd file name except extension) Create a working folder named _leap_tmp, and processing will be done in that folder.
6.13.3. Configure sander¶
Set conditions for executing calculation by sander. Select each item, specify it, and click the [OK] button.
- Basic
- imin
- Specify whether to perform energy minimization.
- igb
- Specify the solvent model.
- ntb
- Specify whether it is a periodic boundary condition or not.
- ntt
- Specify temperature scaling.
- times
- Specify the initial temperature.
- temp0
- Specify the reference temperature.
- I NSTL
- Specify the number of MD steps.
- Advanced
- maxcyc
- Specify the maximum number of cycles.
- NCYC
- Specify the number of cycles using the maximum gradient algorithm.
- gamma_ln
- Specify the collision frequency γ.
- DT
- Specify a time step.
- cut
- Specify the cutoff distance.
- ntpr
- Specify output frequency such as energy value, temperature.
- ntwx
- Specify how often the coordinates are output to the trajectory file.
- QM/MM
- Use qmmm
- Set ifqnt = 1, add &qmmm namelist, and enable the setting for QM/MM/MD calculation.
- qm_theory
- Select the calculation method used in the QM region.
- qmcharge
- Specify the net charge of the QM area.
- qmshake
- Specify the application of the SHAKE method to the H atom in the QM region.
- qm_ewald
- Specify the application of the Ewald method to the QM region.
- qm_pme
- Specify the application of the PME method to the QM region.
- qmmask
- When you press the [Set] button, the atom selected on the main window is set as the QM area. Blue atoms selected by Ctrl + drag on the main window are targeted.
- Misc
- Other Settings
- Write the other settings.
6.13.4. Run sander¶
Run sander. (Crd filename excluding extension) Create a working folder named _amb_tmp, and processing will be done in that folder.
The job is run through Winmostar Job Manager.
6.13.5. Animation¶
Import the coordinates of the trajectory from the PDB file converted from mdcrd file with ptraj.
For the animation display operation method, see Animation window.
6.13.6. Energy Plot¶
Display the energy graph from the calculated log file.
Please see Energy Plot window for how to operate subwindow.
6.13.7. Import Coordinate File¶
Load Amber coordinates (crd) file and topology (prmtop) file and display them in the main window.