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Moloc: Molecular Modelling on UNIX Workstations: 9 Optimizer, All-Atom Force-Field [mab,dab]

Optimizer, All-Atom Force-Field [mab,dab]

This is the basic menu from which to operate the force field MAB [see J.Comp.Aided Design 9, 251-268 (1994)]. It is a tool in the sense that it occurs in several places, but its action may also be considered a separate modelling activity. Whenever a energy calculation is needed the user is dropped into this menu as the last step before the actual calculation.

The energy calculation is performed on all active entries, lumped together in a single molecular aggregate. Visible entries are not affected. A couple of tools, valuable in docking procedures, are also included here for convenience. Most of them are also available in other menus.

The menu name mab or dab indicates whether the user has set the dynamics toggle to energy minimization or to dynamics.

Check H-atom Counts [hyd]

For energy calculations the number of H atoms attached to a heavy atom must be correctly given. Otherwise incorrect bonding situations are taken. In most cases calculations are done with the hydrogens lumped together with their heavy atoms (united atom approach), but the possibility exists to take some or all of them explicitly. In any case the count of H's (explicit and silent ones) must be correct. The present menu serves to modify the number of silent ones. At each atom the current number is indicated. It can be increased by picking the atom with the left mouse button. Decrease (not below zero) is achieved by middle button picks. No checks for unreasonable settings are made. Some file formats have no means to keep this information (e.g. .pdb for HETATMs). When reading such files, usually a routine is invoked, which generates the H-counts from geometrical criteria. In case of poor geometry or unusual chemistry a manual modification may be needed. This option can only be entered with active entries.

Fully paired up electrons are always assumed. Total H- counts that would yield a radical for net charge zero are interpreted as a charged molecule with paired up electrons.

Energy Examination

The energy contributions are graphically displayed. Locations in the structures where large energy contributions are found are colored according to a user definable energy scale.

Set Constraints [ctr]

This menu is used to define constraints of various types in order to influence the course of a energy minimization calculation. Such constraints are useful in various situations such as e.g. flexible matching, docking, etc.

Running a Protocol and Format of Protocol Files

When the batch option is chosen, the user is asked whether he wants to run a sequence of force-field actions given by a protocol. If yes, he is requested to give the name of the protocol file to be applied. This name is written into the control line (Cntl) of the .mab file. The batch job is then guided by this file.

A protocol file is a sequence of lines, each of which determines the action of the force field for the indicated number of steps.

A new protocol instruction is indicated by the keyword Cntl (case is important!). It can be followed by an optional line with the keyword wgts. Both of these lines are also automatically added to a .mab file, whenever a batch job is issued. Thus, an easy way to generate samples of these lines is to start issuing a batch job from Moloc, without submitting it (option q in queue selection).

The control line is read with the following convention:

Cntl idn iter mrep acc stp tmp masf mask fnam(optional)

examples:

Cntl 0 100 0 0.100 1.000 0.5953 3 0

Cntl 1 100 30 0.100 0.500 0.7955 0 0

The parameters have the following meaning (which may be different for minimization and dynamics runs):

The optional line with the keyword wgts has the following form:

wgts MABmask weights

example:

wgts 768 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -99.9 -99.9

As an example the following protocol file leads to a sequence of three dynamics cycles at 400 K with 1000 time steps each, which are followed by energy minimizations. Structures are appended to the result file (.mac) after the minimization step.

Cntl 1 1000 -1 0.100 0.500 0.7955 0 0

Cntl 0 0 0 0.100 0.500 0.7955 0 0

Cntl 1 1000 -1 0.100 0.500 0.7955 0 0

Cntl 0 0 0 0.100 0.500 0.7955 0 0

Cntl 1 1000 -1 0.100 0.500 0.7955 0 0

Cntl 0 0 0 0.100 0.500 0.7955 0 0

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