Energy Calculation Opcodes

The opcodes in this section are linked below:

ELST — Energy LiSTing

DLST — Derivative LiSTing

ASET — Atom SETs

ASNT — turn off Atom Set iNTeractions

VDWB — Van Der Waals Bends

ELST — Energy LiSTing

Calculate energy of current structure and dump Energy LiSTing to one or more output files. Can be used within a BGIN/END loop to compute energies of all structures in a file. ELST cannot be used with the MC conformational searching commands (MCMM, MCSM).

By default, very close nonbonded atomic pairs will be separated before the energy calculation is done. To override this, specify DEBG flag 33. By default the first 100 such pairs encountered are reported unless DEBG flag 36 is specified, then all such pairs are reported. DEBG flag 33, disables the automatic separation of close pairs.

arg1

Extent of listing, format of the output structure file

−1

List the total molecular mechanics energy to the log file only.

Note: For Embrace jobs using the MBAE opcode, Maestro assigns ‑1 as the value for ELST arg1 in the .com file, since using a different value could result in a very large .mmo file.

0

List the total molecular mechanics energy to the log file and the minimal Energy Summary to the file filename.mmo.

1

Write the total molecular mechanics energy to the log file and the complete Energy Listing with all internal coordinate components to filename.mmo.

Note: Setting ELST arg1=1 can result in a very large .mmo file. For certain types of jobs (i.e., those using MBAE), it is recommended that arg1 be set to −1. Otherwise, the .mmo file created could be very large. Alternatively, shorter cutoffs (see EXNB, EXN2, and BDCO) may be used to help keep the .mmo file to a manageable size, if you still wish to have arg1 set to 1.

2

Write double and single precision molecular mechanics energy to log file only. Used for testing or for short summary of total stretch, bend, and other energies.

3

Acts like option 0 except, in addition, numerical and analytical surface areas for all atoms are listed to the .mmo file. Surface energies are also given and are computed using the method specified in arg3.

4

Prints the double precision energy components to the .log file. In the past, this has been possible only in combination with single-precision energies (arg1=2).

arg2

Energy units for log file listing
 

Affects the energies listed in filename.mmo as well as the log file.

0

kJ/mol (default)

1

kcal/mol

arg3

GB/SA solvation numerical area/Born radii options

0

Use numerical evaluations of atomic surface areas and analytical approximation for Born radii (default).

1

Use fast analytical approximations of surface areas and Born radii.

2

Use numerical evaluations of both surface areas and Born radii.

arg4

Updating of interaction array.
 

Non-default options are useful primarily for debugging.

0

(Default.) Program uses internal criteria to decide whether to update the interaction array.

1

Update the full interaction list.

2

Update nonbondeds only.

DLST — Derivative LiSTing

List derivatives for individual atoms to log file. Used for testing. Listed derivatives include first and second derivatives (listings are long so use only on small molecules). When both numerical and analytical derivatives are listed, any discrepancies between analytical and numerical derivatives of more than 5% will be marked by a “*”.

arg1

Derivative selection

1

Numerical and analytical first derivatives (default).

2

Numerical and analytical second derivatives.

3

Numerical and analytical first and second derivatives.

4

Analytical (only) first derivatives.

5

Analytical (only) first and second derivatives.

arg2

Atom number where derivative checking is to begin

0

Start at atom 1 and give derivatives for entire system.

> 0

Start at atom arg2 and give derivatives for rest of system.

< 0

Start at atom 1 and give derivatives for atoms through −arg2.

arg3

Potential function being tested:

0

All (default)

1

Stretch

2

Bend

3

Torsion (proper and improper)

4

Nonbonded

8

Solvation 1

9

Solvation 2

10

Solvation 3

11

Stretch-bend

12

Bend-bend

13

Stretch-torsion

14

Charge-multipole electrostatics

15

Wilson-angle out-of-plane terms

arg4

Number of calls to derivative routine before derivative checking
 

Used for testing of constant derivative options (Default: 1).

arg5

Step length (Angstroms) for numerical derivative calculation
 

Default depends on the potential function selected, but is 0.0001 except for Solvation 1 and Bend-bend.

ASET — Atom SETs

This command is used to place atoms into mutually exclusive sets. During a subsequent ELST procedure (with any ELST arg1 value other than 4) the energy components are printed separately for the interactions within each set, as well as between pairs of sets. Although the sets must be mutually exclusive, they need not, collectively, include all the atoms in the molecule. If DEBG flag 1 is turned on, the set membership is listed in the log file at the time of the ELST command.

The various ASET energies are a pairwise breakdown of the interaction energies obtained by adding up the individual atom-atom interaction energies. This approach has difficulties with GB/SA solvation because it is not a pairwise additive potential. In the generalized Born (GB) approach the solvation energy depends on the Born radii each of which depend in a complex way on the arrangement of large number of atoms in the system. The ASET mechanism takes a static approach to calculating the GB solvation energy in which this dependence of the Born radii is ignored, leaving a simple pairwise sum of solvation terms. The surface area (SA) portion of the solvation energy calculation is more problematic because from a single conformation it is not obvious how much the surface area is affected by association. Also, because the solvent inaccessible regions are often excluded by multiple atoms, a pairwise breakdown of the energy solvation energy is problematic. The ASET mechanism takes a simple approach in that it associates the SA solvation term with the interaction of a set with itself.

ASET commands may be issued before a READ, and are in force for all subsequent structures read until or unless cleared or altered. Thus, such commands may be issued before a BGIN/END loop, and will be in force for all structures read within the loop.

Arg7 and arg8 are only used when MBAE is not used.

arg1-4

Atom number
 

The action that is applied to these atoms depends on the settings of arg5 and arg6. If arg1-4 are all zero, then the action is applied to all atoms in the system.

arg5

Set number
 

May be any non-negative integer, specified as 0.0000, 1.0000, 2.0000, etc. Only sets one through 20 will be considered during a subsequent ELST. Set 0 stands for no set; placing an atom in Set 0 is the equivalent of removing it from whatever set it had been in. Recall that the sets are non-overlapping: an atom is a member of only the last set into which it is placed.

arg6

Command mode
 

Should be given <an integer value (such as −1.0000). This argument is used to specify the action to be taken, as follows:

0

Add the listed atoms to the set.

1

Synonym for 0.

−1

Delete the listed atoms from the set given, if they are in the set. Attempts made to delete atoms from set 0 are ignored.

2

Add the range of atoms between arg1 and arg2 (inclusive) to the set; arg3 and arg4 are ignored.

−2

Delete each atom in the given range from the set, provided it is in the set.

3

Add the molecules containing the atoms given by args1 through 4 to the given set.

−3

Delete the molecule containing the atoms in args1 through 4 from the set, if they were in it.

arg7

Property for inter/intra set energies
 

Write inter-set or intra-set interaction energies as properties to the structure output file. Should be given an integer value (such as 2.0000).

0

Inter-set energies between set 1 and all other sets (default).

2

Inter-set energies between all sets.

4

Intra-set energies for all sets.

arg8

Select energy components
 

Select the energy components that are written as properties to the structure output file. Should be given an integer value (such as 2.0000).

0

Record only the total energy (default).

2

Record the total energy and non-bonded energy.

4

Record all energetic components.

ASNT — turn off Atom Set iNTeractions

This command allows energetic interactions between sets to be turned on and off. The sets must be defined using the ASET command. Separate control is available over force-field interactions and constraint interactions imposed using the FXDI, FXBA, and FXTA commands.

ASNT commands may be issued before a READ, and are in force for all subsequent structures read until or unless cleared or altered. Thus, such commands may be issued before a BGIN/END loop, and will be in force for all structures read within the loop.

arg1

Set number or control

> 0

The first set number.

<0

The actions encoded in arg3 and arg4 will be applied to all pairs of sets.

arg2

Set number or control

> 0

The second set number.

< 0

The actions encoded in arg3 and arg4 will be applied pairwise to all set combinations including the set encoded in arg1, which must be positive.

arg3

Force-field interaction control

0

Turn off force-field interactions between sets.

1

Leave force-field interactions on.

arg4

Constraint-interaction control

0

Turn off constraint interactions between sets.

1

Leave constraint interactions on.

Examples:

  • ASNT 1 2 0 0: Turns off all interactions between sets 1 and 2.

  • ASNT 1 2 0 1: Turns off force-field interactions but retains constraint interactions between sets 1 and 2.

  • ASNT 2 -1 0 0: Turns off all interactions between set 2 and other sets.

  • ASNT −1 0 1 1: Turns on all interactions between all sets (i.e., restores initial state of the program).

    VDWB — Van Der Waals Bends

Used to model the coordination sphere of an inorganic complex, using the “points-on-a-sphere” model as described by Hay [24]. In this model, the mutual interaction of a pair of ligands bound to the same metal is handled by means of a van der Waals, rather than bond-angle-bending interaction. This command replaces specified bond-angle interactions with van der Waals interactions.

Note: Coulombic components are removed from these interactions, unless DEBG 12 is specified.

VDWB may be used along with the MCMM, LIGB, and MOLS commands to perform a configurational search of the coordination sphere. TORS and, if applicable, RCA4 commands can be added to explore the internal conformational space of the ligands at the same time.

arg1

Central atom
 

Typically, the metal atom. Bends about this atom are replaced with vdW interactions.

arg2

Outer atom

0

All bends with arg1 as the central atom with be replaced with vdW interactions.

> 0

Arg3 must also be greater than 0. In this situation, the arg2-arg1-arg3 bond will be replaced by a vdW interaction.

< 0

Arg3 must also be less than 0. In this situation, if arg1 already has some bends on the VDWB list, the ABS(arg2)-arg1-ABS(arg3) bend is removed. If no such list exists for arg1, one is created and all bends centered on arg1 are placed on it except ABS(arg2)-arg1-ABS(arg3).

arg3

Outer atom
 

See arg2 description.

arg5,6

ro and ε for the van der Waals pairs modeled by VDWB.
 

If these are specified, all pairs will be modeled using the same parameters: the last nonzero values specified in any VDWB command. If ro and ε are not specified, atom-type-dependent van der Waals parameters from the force-field are used. To achieve a nearly purely repulsive potential, use, for example, ro = 9.0 and ε = 1.0E−6. This is nearly identical to the repulsive part of a MacroModel C1-C1 nonbonded interaction using the AMBER force field. Our own experience indicates that default parameters (arg5 = arg6 = 0) give good results.