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 are shown. At this time, it's possible to
manage the energy minimization and conformational search 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.
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To perform an energy minimization,
select Minimization in the Calculate -> Ammp menu. 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). |
8.2.2 AMMP conformational search
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To perform a conformational search,
select Conformational search in the Calculate -> Ammp menu.
In the Search parameters box, you can select the search method (Method
combo-box): Systematic,
Random and
Boltzmann jump. |
Highlighting one or more torsions in the
list, you can change the parameters (Base, Steps and Window)
in the Torsion parameters box. Not all field 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 the 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 the 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.
Warning: it's strongly recommended to 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:
Open or build the molecule. If you want use the SP4 force field (recommended), check if the bond types (bond order) are correctly assigned. If it's not true, select Edit -> Change -> Bonds in the main menu, choose Find the bond types, click Apply.
Fix the atom types (optional) and the charges (Calculate -> Charge & Pot.).
If the starting geometry isn't minimized, before the conformational search, perform a full minimization. To do it, open the minimization dialog window (Calculate -> Ammp -> Minimization), uncheck the outputs (Trajectory, Output and Energy), select Conjugate gradients, 3000 steps, 0.01 toler, 0 steepest steps and finally click the Run button.
Open the conformational search dialog window (Calculate -> Ammp -> Conformational search).
Add all flexible torsions clicking the Edit torsion buttons. For more information about the selection tool click here.
In the Search parameters box, set Method = Boltzmann jump, Steps = 1000 (default value), Temp. = 1000 and RMSD = 60 (default value).
Check Minimize all conformations, Steps = 50, Toler = 0.01 (default value).
Check Trajectory, Output and Energy outputs. Change the default file name and or the trajectory format if it's required by you.
Click the Run button.
At the end of the calculation, three files will be obtained: a trajectory file (the trajectory analysis tool can open it), an output file containing all messages printed in the console by AMMP and an energy file in CSV format (the first value is the conformation number and the second one is the energy).
The resulting conformations can be finally clustered (see Trajectory analysis).
8.2.3 AMMP console
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In the Console tab, it's
possible to control AMMP sending direct 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. |
8.2.4 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. |
8.2.5 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. 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 the 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 can be placed custom parameter files:
*_vega.inp are created by the VEGA team to expand the standard parameter
capabilities and *_user.inp can be generated by the users when the
parameters are missing in the standard parameter file.
When a non-SP4 force field is selected for an AMMP calculation, 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
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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. |