8.2 AMMP calculation

AMMP is a modern full-featured molecular mechanics, dynamics and modelling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP. For more information, see the AMMP manual.

Selecting Calculate -> Ammp in the VEGA ZZ menu bar, the AMMP dialog windows is shown. At this time, it's possible to manage the energy minimization only, but the other calculation modes are accessible trough the AMMP direct commands (see the AMMP manual).
Please remember that before to perform an AMMP calculation, the atom charges must be assigned (for more information click here). The atom types, if not already assigned, are automatically recognized. If you find problems in the automatic assignment, you can proceed to fix them assigning the atom types using the Calculate -> Charge & Pot. menu item (SP4 force field) or the manual function (Edit -> Change -> Atom/Residue/Chain).

WARNING:
The SP4 force field is atom-oriented: it means that the force constants are computed starting from the atoms parameters and they aren't in angle, bond, torsion and improper tables. To compute that constants, the bond order is required. The optimization of molecules with wrong bond types (single, partial double, double and triple) could carry out to a bad structure. If you need to fix the bond types, select Edit -> Change -> Bonds in the menu bar, choose Find the bond types and finally click the Apply button (for more details, click here).
The bond order is automatically checked before starting the minimization. If a problem is found, a warning dialog window is shown by which it's possible to ignore the problem or to abort the procedure highlighting the atoms with the possible wrong bond order.

 

8.2.1 Energy minimization

Minimization   

In the Minimization tab, you can change the main minimization parameters and the minimization algorithm: Single point, Steepest descent, Trust, Conjugate gradients, Quasi-Newton, Truncated Newton, Genetic algorithm, Polytope symplex and Rigid-body. The Graphic update field sets the number of iterations after which the VEGA ZZ 3D view is refreshed (nupdat variable).
When you start the minimization clicking the Run button, the calculation steps and the error messages are shown in the VEGA ZZ console. If you want stop the interactive run, you must click with the right mouse button on the workspace area and select Stop calculation.
To revert to the default parameters, click the Default button.

 

8.2.2 AMMP console

Console   

In the Console tab, it's possible to control AMMP sending directly the commands. This function is useful to perform operations not implemented trough the graphic user interface or to get/set the system variables. The output is always redirected to the VEGA ZZ console.
The commands must be typed in the bottom box and confirmed clicking Send or pressing the return key. The top box is the command history containing the latest typed commands. They can be repeated double clicking the line.

 

8.2.3 Calculation parameters

Parameters   

The Parameters tab allows to change the Dielectric constant (dielect variable), the Long range cutoff (cutoff variable), the Short range cutoff (mxcut variable), the Update full electrostatic threshold (mxdq variable), the Lambda value for homotopic force field terms (lambda variable) and Random number seed (seed variable). This value is used to initialize the pseudo-random number generator.
In the Constraints box, it's possible to enable the use of the constraints defined by the Atom constraints function: None makes all atoms free without constraints,  Atom fixing keep the atoms totally fixed (see ACTIVE and INACTIVE commands) and Tethering allows little movements around the starting position of the atoms depending on the force constant (see TETHER command).
To revert to the default parameters, click the Default button.

 

8.2.4 Potential terms

Potential   

In the Potential tab, it's possible to change the potential terms used for the energy evaluation. For more details, see the AMMP's USE command. The Edit box contains two buttons: the Template button allows to change the SP4 ATDL template used for the atom type recognition, the Parameters button allows to change the SP4 potential parameters. To revert to the default parameters, click the Default button.

 

8.2.5 Hosts

Hosts   

AMMP can be executed on local and remote hosts according to the VEGA ZZ calculation host concept (for more information, click here). If you select a local host, the calculation is executed using the local hardware, otherwise is executed on a remote host. Host pools allows to filter the host list and the default pools are: All hosts, Local hosts and Remote hosts. Other polls can be defined by the user for massive parallel calculations not yet implemented.
Selecting Localhost the calculation is immediately executed in interactive mode (if you close VEGA ZZ, the job is stopped); selecting Localhost background, the calculation is started in background and it can't be controlled by VEGA ZZ (if you close VEGA ZZ, the job continues without stopping itself); selecting Localhost save file, the calculation is not started and the input file is created to run the job later.
Please note the duplicated hosts: they are child hosts and they are assigned one for each physical or virtual CPU (for more information, click here).
The Edit button allows to open the host configuration window.