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 an item in the Calculate Ammp menu, the AMMP dialog windows is shown. At this time, it's possible to do energy minimization and conformational search only, but 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 don't need to be assigned, because they are automatically recognized every time that a calculation starts. 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. Optimizations of molecules with wrong bond types (single, partial double, double and triple) could carry out to bad structures. 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 types are 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

To perform an energy minimization, select Minimization in Calculate Ammp menu.

 

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 simplex 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 VEGA ZZ console. If you want to stop the interactive run, you must click with the right mouse button on the workspace area and select Stop calculation. In the same way, it's possible to shutdown the system when the calculation is finished, checking Power off the system.
Is it possible to save the Trajectory, the Output messages generated by AMMP and shown in the console, the Energy for each trajectory frame and the Velocities (this option isn't yet available), enabling the each field clicking the checkbox. To change the file names and the file formats, click the disk button Disk button.

 

Output files

 

If you are changing the trajectory file name, the Save trajectory file requester is shown, in which you can select the trajectory file format (for more information click here). To copy the file name to all fields, click the small button Copy file name button at the left of the disk button. To revert to the default parameters, click the Default button.

 

WARNING:

the fields of output files are automatically filled using the file path of the last loaded molecule and the name of the current workspace. If you change the current workspace, the file names are updated and manual changes are lost.

 

8.2.2 AMMP conformational search

To perform a conformational search, select Conformational search in Calculate Ammp menu.

 

Conformational search

 

In Search parameters, you can select the search method (Method combo-box): Systematic, Random and Boltzmann jump.
As first step, you must select the torsion (dihedral) angles that will be considered during the conformational search. To do it, press the Edit torsions button: the Selection tool dialog window will be shown. You can also load the selection by drag & drop of a file or by context menu (Open menu item). By this tool, you can choose all or flexible or user defined torsions and the list is automatically updated in the conformational search windows also. For each torsion, the name (Torsion), the starting value in degrees (Base), the number of rotation steps for the systematic search (Steps) and the range in degrees in which the random rotations are computed (Window) or ending rotation value (End) when you perform the systematic search. The checkbox at the beginning of each line allows to consider or not the torsion in the calculation. With the context menu, you can un/check all torsions (Check all, Uncheck all), un/check the highlighted/selected torsions (Check selected, Uncheck selected) and un/select all torsions (Select all, Unselect all). Highlighting one or more torsions in the list, you can change the parameters (Base, Steps and Window) in the Torsion parameters box. Not all parameter fields are enabled at the same time and that's related to the type of the search that you selected (see Method combo-box).
Checking Minimize all conformations, a conjugate gradients minimization is performed for each generated conformation. You can set the number of minimization steps (Steps) and toler value (Toler). Generally it's strongly recommended to enable this option.
Choosing the random search method, the Steps field in the Search parameters box is enabled, in which you can specify the number of random conformations that will be generated. In the Apply to box, you can decide to apply the random rotation to the starting conformation (none checked), to the previous generated conformation (Previous checked) and to the previous minimized conformation (Previous and Minimized checked). If Minimize all conformations is not checked, the meaning of this last option is the same of Previous checked only.
Choosing the Boltzmann jump method, the Steps, Temp. and RMSD fields are enabled: Steps allows to specify the number of conformations that will be generated, Temp. is the temperature in Kelvin and RMSD is the torsion root mean square difference (in degrees) used in the Boltzmann jump perturbation phase to generate a significant different conformation compared to the previous one.
Clicking the Run button, the conformational search begins and at the end the lowest energy structure is kept in the workspace.

Some operations, shown in the next table, can be done by the context menu that can be displayed by clicking with the right mouse button on the torsion list:

 

Item Subitem SubSubItem Description
Open - - Open a torsion selection (for more information, see the Selection tool).
Save as ... - - Save the torsions to a file.
Fill Base & end 5 Systematic:

complete automatically Base and End fields of each highlighted torsion with the range obtained from the current torsion angle adding and subtracting the selected value.

 

Random and Boltzmann jump:

complete automatically Base and Window fields of each highlighted torsion respectively with the current torsion angle and the double of selected value.

 

 

10
20
30
45
60
90
120
80
Base with torsion value - Complete automatically the Base field of each highlighted torsion with the current torsion value.
Current values - Set Base, Steps and Window/End fields of each highlighted torsion with the values in the Torsion parameters box.
Default - Set Base, Steps and Window/End fields of each highlighted torsion with the default values (respectively 0.00, 6, 360.00).
Check all - - Check/enable all torsions.
Check selected - - Check/enable the selected torsions.
Uncheck all - - Uncheck/disable all torsions.
Uncheck selected - - Uncheck/disable the selected torsions.
Select all - - Select all torsions.
Unselect all - - Unselect all torsions.

 

WARNING:

it's strongly recommended to set the Graphic update to 1, otherwise not all conformations are saved in the output file, but only one every N conformations, where N is the graphic update value.

 

8.2.2.1 Conformational search example

Imagine to perform a conformational search of a small molecule using the Boltzmann jump method:

 

8.2.3 AMMP console

In the Console tab, it's possible to control AMMP sending direct commands.

 

Console

 

This function is useful to perform operations not implemented in the graphic user interface or to get/set the system variables. The output is always redirected to 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.

 

8.2.4 Calculation 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.

 

Parameters

 

In 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 force constants (see TETHER command).
To revert to default parameters, click the Default button.

 

8.2.5 Potential terms

In Potential tab, it's possible to change the potential terms used for the energy evaluation.

 

Potential

 

For more details, see the AMMP's USE command. In the Force field box, you can change the force field type used by AMMP: SP4 (the standard AMMP force field) and CHARMM 22. The Template button allows to change the ATDL template used for the atom type recognition, the Parameters button allows to change the potential parameters. To revert to default parameters, click the Default button.

 

8.2.5.1 Non-SP4 force fields

The parameter files of these force fields must be in the standard CHARMM/NAMD format. They must placed in the VEGA ZZ\Data and in the VEGA ZZ\Data\Parameters directories and they must have the .inp extension. For the automatic atom type assignment, for each .inp file must exist a .tem file containing the ATDL tremplate (e.g. CHARMM22_PROT.inp and CHARMM22_PROT.tem). The parameter files interpreter included in the HyperDrive library has the pre-processor feature to include more files:

*
* CHARMM 22 parameters file for VEGA ZZ
*
INCLUDE "Parameters/par_all22_lipid.inp"
INCLUDE "Parameters/par_all22_na.inp"
INCLUDE "Parameters/par_all22_prot.inp"
INCLUDE "Parameters/par_all22_vega.inp"
INCLUDE "Parameters/par_all22_user.inp"

WARNING:

no error message is shown if the included file doesn't exist. In the VEGA ZZ\Data\Parameters directory, custom parameter files can be placed: *_vega.inp are created by the VEGA team to expand the standard parameters and *_user.inp can be generated by users when the parameters are missing in the standard files.
When a non-SP4 force field is selected, is it possible that one or more parameters are missing and so the missing parameter table is shown in order to allow to the user to add the missing parameter.

 

8.2.6 Hosts

AMMP can be executed on local and remote hosts according to the VEGA ZZ calculation host concept (for more information, click here).

 

Hosts

 

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.