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
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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). |
8.2.2 AMMP console
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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. |
8.2.3 Calculation parameters
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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. |
8.2.4 Potential terms
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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
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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. |