# zerom (c47b2)

The Z Module is a general facility for carrying out conformational

searches based on rigid-geometry mapping or so-called "zero-order"

minimization. It also includes 1st-order minimization methods (Steepest

Descent and Conjugant Gradient), but the fundamental structure of the method

is nonetheless grid-based.

Reference:

RJ Petrella, M Karplus. "A Versatile Deterministic Method for Conformational

Searches: Application to CheY" (to be published).

* Method | Z Method

* Syntax | Syntax of the ZMOD command

* Description | Description of the various subcommand functions

* Examples | Usage examples

* Supplementary | More complex searches

searches based on rigid-geometry mapping or so-called "zero-order"

minimization. It also includes 1st-order minimization methods (Steepest

Descent and Conjugant Gradient), but the fundamental structure of the method

is nonetheless grid-based.

Reference:

RJ Petrella, M Karplus. "A Versatile Deterministic Method for Conformational

Searches: Application to CheY" (to be published).

* Method | Z Method

* Syntax | Syntax of the ZMOD command

* Description | Description of the various subcommand functions

* Examples | Usage examples

* Supplementary | More complex searches

Top

The Z Method

The Z method depends on a partitioning of the conformational space of

a system into subsystems or "subspaces", where a subspace is a subset of all

the degrees of freedom in the system. Once defined, the subspaces can be

searched independently or in combinations. Specifically, the facility searches

all N!/(N-n)!n! combinations of N subspaces taken n at a time, where N and n

are any positive integers, and n<=N. Each grid or combination searches a

set of n subspaces having C(1),C(2),...C(n) conformations across a total of

C(1)*C(2)*...C(n) conformations. For example, if there are 4 subspaces, each

containing 20 conformers, taking 2 subspaces at a time would produce 6 grids

(4!/2!2!), each with 400 grid-points or energy calculations. The overall

search results in a subspace, the "product subspace", that is the union of all

the starting or "reactant" subspaces. Hence, when n > 1, the product subspace

is always larger than each of the reactant subspaces. For each grid, the

subspaces not being searched are held fixed at their initial conformations

(internal coordinate values occurring in the IC table prior to any of the

grid searches having been done). The conformers resulting from the search

may be written to a .dcd ("trajectory") file or to an output conformer file.

The latter is formatted in such a way as to allow it to be used as an input

conformer file in subsequent searches.

In the current implementation, the degrees of freedom are internal

coordinates, although they could, in principle, include Cartesian coordinates

as well. The degrees of freedom--proper or improper dihedral angles, bond

angles, or bond lengths--must be defined. Then, conformers for each subspace

are read from one or more input conformer files, which contain lists of the

degrees of freedom, their possible values, and corresponding subspace numbers.

Hence, the input conformer files define the subspaces as well as specifying

their possible conformations.

Before beginning the search, the N subspaces to be searched must be

"loaded." This loading feature allows for searching various parts of the

system without having to redefine substructures or change the numbering of

subspaces--i.e. all the substructures/subspaces may be defined once and then

subsets can be selected for inclusion in the searches by use of the loading

feature.

A subspace has associated with it an atomic "substructure", which is

comprised of the atoms that are to be included in the energy calculations.

For each overall search, the set of atoms included in the calculation is the

union of the sets of atoms in all of the loaded subspaces. Hence, for a

given subspace combination, or grid, within the larger search, atoms

corresponding to subspaces not being searched are also included in the

calculation. Note that an atom can be (and usually is) a part of multiple

substructures, but in general, a degree of freedom should not be a part

of multiple subspaces.

Subspaces can be searched in multiple regions. For the sake of

simplicity, this is done essentially by replicating subspaces, rather than by

the use of a separate "region" layer in the hierarchical formalism of the

method. This means that rather than assigning a subspace two search regions,

the subspace is simply replicated and the two resulting subspaces are then

assigned to different categories or types. A search can be done over all

N!/M!m!(N-M-m)! combinations of the N subspaces, taken M + m at a time, where

M is the number of subspaces being searched in the first region and m is the

number of subspaces being searched in the 2nd (or "minor") region. This is

discussed separately below under Supplementary.

In an attempt to optimize its utility, the Z module is designed to be

able to be entered and exited easily and often over the course of a single

charmm script. This allows sections of Z module commands in CHARMM scripts

to be conveniently interspersed with other CHARMM commands and functions.

Note, however, that some standard miscellaneous CHARMM commands, such as

the DEFIne, SET, and CALC commands, and the OPENing of units for writing

output, are supported within the Z module, itself.

Distance and degree-of-freedom constraints may be defined, and then

selected ones may be used (loaded) in a given search. For each new

conformation, the loaded distance constraints (if they exist) are checked

against the structure. If the conformer satisfies all of the distance

constraints, then the loaded degree-of-freedom constraints are checked. If

the degree of freedom constraints are all satisfied, then the energy

calculation on that conformer is done.

Z module searches result in changes in the main coordinate set as

well as in the main IC table.

Other Notes:

- At the start of the Z module run, the ZMEMory command must be given

so as to allocate the memory for the run.

- The Z module uses the CHARMM internal coordinate tables. Hence, in

order for the module to function, 1) an IC table must be present, having

either been generated (GENErate ... SETup command) or read in

(READ IC command); and 2) the IC FILL command must be given.

This command fills the IC table with internal coordinate values derived

from the Cartesian coordinates in the main coordinate set (see also

intcor.info).

- The Z module requires the use of the BYCC list-builder (BYCC keyword in

the NBONDs or UPDAte command).

- Note that the Z module modifies the active atom lists, so that the

NBACtive and BACTive commands (which specify the atoms to be considered

in the non-bonded and bonded energies, respectively) should be invoked

after exiting the module and before calculating CHARMM energies or forces

with non-Z-module commands. The same is true for the fixed atom list:

the CONS FIX command should be invoked if the CFIX keyword has been used

in the Z module searches (i.e. in the ZSEArch command).

- For the Z module to function properly, The CHARMM code must be compiled

with the ACTBOND and ZEROM keywords in the precompiler keyword list file

(build/xxx/pref.dat). The NOBYCC and GENETIC precompiler keywords cannot be

used with the Z module (ZEROM). The GENETIC and ACTBOND keywords are

incompatible.

- The Z module currently supports CMAP, but not for SD or CONJ minimizations.

It does not support the implicit solvation models, (ACE, GB, etc.) except

for EEF1.

It is not currently parallel.

The Z Method

The Z method depends on a partitioning of the conformational space of

a system into subsystems or "subspaces", where a subspace is a subset of all

the degrees of freedom in the system. Once defined, the subspaces can be

searched independently or in combinations. Specifically, the facility searches

all N!/(N-n)!n! combinations of N subspaces taken n at a time, where N and n

are any positive integers, and n<=N. Each grid or combination searches a

set of n subspaces having C(1),C(2),...C(n) conformations across a total of

C(1)*C(2)*...C(n) conformations. For example, if there are 4 subspaces, each

containing 20 conformers, taking 2 subspaces at a time would produce 6 grids

(4!/2!2!), each with 400 grid-points or energy calculations. The overall

search results in a subspace, the "product subspace", that is the union of all

the starting or "reactant" subspaces. Hence, when n > 1, the product subspace

is always larger than each of the reactant subspaces. For each grid, the

subspaces not being searched are held fixed at their initial conformations

(internal coordinate values occurring in the IC table prior to any of the

grid searches having been done). The conformers resulting from the search

may be written to a .dcd ("trajectory") file or to an output conformer file.

The latter is formatted in such a way as to allow it to be used as an input

conformer file in subsequent searches.

In the current implementation, the degrees of freedom are internal

coordinates, although they could, in principle, include Cartesian coordinates

as well. The degrees of freedom--proper or improper dihedral angles, bond

angles, or bond lengths--must be defined. Then, conformers for each subspace

are read from one or more input conformer files, which contain lists of the

degrees of freedom, their possible values, and corresponding subspace numbers.

Hence, the input conformer files define the subspaces as well as specifying

their possible conformations.

Before beginning the search, the N subspaces to be searched must be

"loaded." This loading feature allows for searching various parts of the

system without having to redefine substructures or change the numbering of

subspaces--i.e. all the substructures/subspaces may be defined once and then

subsets can be selected for inclusion in the searches by use of the loading

feature.

A subspace has associated with it an atomic "substructure", which is

comprised of the atoms that are to be included in the energy calculations.

For each overall search, the set of atoms included in the calculation is the

union of the sets of atoms in all of the loaded subspaces. Hence, for a

given subspace combination, or grid, within the larger search, atoms

corresponding to subspaces not being searched are also included in the

calculation. Note that an atom can be (and usually is) a part of multiple

substructures, but in general, a degree of freedom should not be a part

of multiple subspaces.

Subspaces can be searched in multiple regions. For the sake of

simplicity, this is done essentially by replicating subspaces, rather than by

the use of a separate "region" layer in the hierarchical formalism of the

method. This means that rather than assigning a subspace two search regions,

the subspace is simply replicated and the two resulting subspaces are then

assigned to different categories or types. A search can be done over all

N!/M!m!(N-M-m)! combinations of the N subspaces, taken M + m at a time, where

M is the number of subspaces being searched in the first region and m is the

number of subspaces being searched in the 2nd (or "minor") region. This is

discussed separately below under Supplementary.

In an attempt to optimize its utility, the Z module is designed to be

able to be entered and exited easily and often over the course of a single

charmm script. This allows sections of Z module commands in CHARMM scripts

to be conveniently interspersed with other CHARMM commands and functions.

Note, however, that some standard miscellaneous CHARMM commands, such as

the DEFIne, SET, and CALC commands, and the OPENing of units for writing

output, are supported within the Z module, itself.

Distance and degree-of-freedom constraints may be defined, and then

selected ones may be used (loaded) in a given search. For each new

conformation, the loaded distance constraints (if they exist) are checked

against the structure. If the conformer satisfies all of the distance

constraints, then the loaded degree-of-freedom constraints are checked. If

the degree of freedom constraints are all satisfied, then the energy

calculation on that conformer is done.

Z module searches result in changes in the main coordinate set as

well as in the main IC table.

Other Notes:

- At the start of the Z module run, the ZMEMory command must be given

so as to allocate the memory for the run.

- The Z module uses the CHARMM internal coordinate tables. Hence, in

order for the module to function, 1) an IC table must be present, having

either been generated (GENErate ... SETup command) or read in

(READ IC command); and 2) the IC FILL command must be given.

This command fills the IC table with internal coordinate values derived

from the Cartesian coordinates in the main coordinate set (see also

intcor.info).

- The Z module requires the use of the BYCC list-builder (BYCC keyword in

the NBONDs or UPDAte command).

- Note that the Z module modifies the active atom lists, so that the

NBACtive and BACTive commands (which specify the atoms to be considered

in the non-bonded and bonded energies, respectively) should be invoked

after exiting the module and before calculating CHARMM energies or forces

with non-Z-module commands. The same is true for the fixed atom list:

the CONS FIX command should be invoked if the CFIX keyword has been used

in the Z module searches (i.e. in the ZSEArch command).

- For the Z module to function properly, The CHARMM code must be compiled

with the ACTBOND and ZEROM keywords in the precompiler keyword list file

(build/xxx/pref.dat). The NOBYCC and GENETIC precompiler keywords cannot be

used with the Z module (ZEROM). The GENETIC and ACTBOND keywords are

incompatible.

- The Z module currently supports CMAP, but not for SD or CONJ minimizations.

It does not support the implicit solvation models, (ACE, GB, etc.) except

for EEF1.

It is not currently parallel.

Top

Syntax of the ZMOD command

[ZMOD functions SYNTAX]

ZMOD enter the Z module

END exit the Z module

Subcommands Keywords

ZMEMory NDOFs {int} NSUBspaces {int} NCONFormers {int} NVALues {int}

NATOm {int} CSIZe {int} NDIStances NDAToms NDFConstraints MXLN {int}

ZDEFine DOFR {int} internal coordinate specification

{ATOM SELECTION X 2} REVErse

/

SUBStructure {int} or

\

ALIAs {int}

DIST {int} {ATOM SELECTION X 2} GTHAn {REAL} LTHAn {REAL}

DFCO {int} DOF {int} GTHAn {REAL} LTHAn {REAL}

ZREAd CONF RUNI {int} WUNI {int} MISSing REDUndant SSDIsorder

ZLOAd NULL SUBS {int1 int2 int3 ... } CLEAR

DIST {int1 int2 int3 ... } CLEAR

DFCO {int1 int2 int3 ... } CLEAR

ZSPECifications

ZSEArch TAKE {int} WRUN {int} ECUT {real} VCUT {real}

WCOM MINA SPECifics CFIX MSD NOOR WDUN NDST

SD {int} CONJ {int}

ZMIN LOAD

ZSET

ZRANdom SEED {int} WUNI {int} ECUT {real} VCUT {real}

SUBS {intI1 intJ1 intI2 intJ2 intI3 intJ3...} or

SUBS ALLSubspaces {int}

ZFIL ECUT {real} VCUT {real} VLCUT {real} WUNI {int}

LECUt {intI1 intJ1 intI2 intJ2 intI3 intJ3...} END

Syntax of the ZMOD command

[ZMOD functions SYNTAX]

ZMOD enter the Z module

END exit the Z module

Subcommands Keywords

ZMEMory NDOFs {int} NSUBspaces {int} NCONFormers {int} NVALues {int}

NATOm {int} CSIZe {int} NDIStances NDAToms NDFConstraints MXLN {int}

ZDEFine DOFR {int} internal coordinate specification

{ATOM SELECTION X 2} REVErse

/

SUBStructure {int} or

\

ALIAs {int}

DIST {int} {ATOM SELECTION X 2} GTHAn {REAL} LTHAn {REAL}

DFCO {int} DOF {int} GTHAn {REAL} LTHAn {REAL}

ZREAd CONF RUNI {int} WUNI {int} MISSing REDUndant SSDIsorder

ZLOAd NULL SUBS {int1 int2 int3 ... } CLEAR

DIST {int1 int2 int3 ... } CLEAR

DFCO {int1 int2 int3 ... } CLEAR

ZSPECifications

ZSEArch TAKE {int} WRUN {int} ECUT {real} VCUT {real}

WCOM MINA SPECifics CFIX MSD NOOR WDUN NDST

SD {int} CONJ {int}

ZMIN LOAD

ZSET

ZRANdom SEED {int} WUNI {int} ECUT {real} VCUT {real}

SUBS {intI1 intJ1 intI2 intJ2 intI3 intJ3...} or

SUBS ALLSubspaces {int}

ZFIL ECUT {real} VCUT {real} VLCUT {real} WUNI {int}

LECUt {intI1 intJ1 intI2 intJ2 intI3 intJ3...} END

Top

ZMOD Subcommand Description

-------------------------------------------------------------------------------

ZMOD

END

Enter (ZMOD) and exit (END) the Z module.

-------------------------------------------------------------------------------

ZMEMory

Allocates memory for the entire module. It and several subcommands must be

specified before any other ZMOD subcommands are given. NDOFs is the number of

degrees of freedom to be defined in the system; NSUBspaces is the number of

subspaces/substructures to be defined; NCONFormers is the total number of

conformers in all subspaces to be read in via conformer files; NVALues is the

cumulative length of all conformer files (total number of degree of freedom

values, one value per line) to be read in; NATOM is the total number of atoms

in all substructures (since atoms can occur in multiple substructures, this

number may exceed the total number of atoms in the system); CSIZe is the

maximum number of degrees of freedom that occur in any one conformer

(optional). NDIST is the number of distance constraints (required only

if distance constraints are being used). NDAToms is the total number of atoms

used in all of the distance constraints (required only for distance

constraints). NDFConstraints is the number of degree-of-freedom constraints

(required only for use of DOF constraints the degrees of freedom (DOFR),

the substructures (SUBS), distance constraints (DIST), and internal coordinate

constraints (DFCO) which must all be numbered serially from 1. The degrees

of freedom (DOFR) syntax is similar to that for editing the IC table

(see IC EDIT), and involves either bond distances (BOND), bond angles (ANGL),

or improper or proper dihedral angles (DIHE). The IC table should have been

filled "IC FILL" prior to the ZDEFine DOFR command. Importantly, when a degree

of freedom (DOFR subcommand) is thus defined, its initial value from the IC table

is stored and used as a default value when the subspace containing that degree

of freedom is included among the N subspaces in a search but is not one of

the n subspaces being searched on the current grid.

Although the degree-of-freedom definitions can be changed easily with the

ZDEFine DOFR command, for convenience, the design of the Z module is

intended to allow the user to define all the necessary degrees of freedom

initially, and then to perform all searches on the basis of that initial set of

definitions.

The MXLN subcommand can be used in parallel execution to increase memory associated

with the handling of data output

-------------------------------------------------------------------------------

ZDEFine

The substructure definition contains two atom selections: the first

defines the atoms that make up the substructure, and the second defines

the moving atoms--i.e. the atoms whose positions are to be initialized and

rebuilt during the searches. By default, the Cartesian coordinates are built

from the internal coordinates in the order of the atom numbers in the

substructure, lowest to highest. The REVErse subcommand causes the substructure

to be built up in the opposite sense, from higher atom number to lower. This

reversal is applied only to those substructures to which the subcommand is

assigned (and their aliases). The "REVErse" subcommand is often necessary, for

example, in building up loop structures from N-terminal and C-terminal halves.

(The alternative to explicitly defining a substructure is to define it

as an alias of another one by use of the subcommand "ALIAs {int}."

This is useful in combination with the ZCATegorize MINOR and ZSEARCh MINOR

commands to search the same subspace in two different regions.

See Searching Subspaces in Two Regions, below.)

The distance constraint definitions also contain two atom selections

each. Each constraint is applied to the distance between the centers of

geometry of the two selections. The distance constraint number

(serially ordered from 1), two atom selections, and upper and lower distance

bounds must be given for each distance constraint.

The internal coordinate or DOF constraint (DFCO) definitions require the

specification of the DOF constraint number as well as the integer corresponding

to the actual degree of freedom as defined in the ZDEFine DOF commands. The

upper and lower bounds for the constraints (in degrees) must also be specified.

The constraints are currently implemented for dihedral, improper, and bond

angles (not bond lengths). The bounds must be in the interval [-360,360]. This

feature is intended for applying constraints to degrees of freedom that are not

explicitly being searched. A good example occurs in loop searches, in which

both halves of the loop are being searched together for low-energy

combinations. The dihedral between the two searched halves of the loop is not

explicitly being searched (it doesn't exist in either half of the loop), but it

may need to be constrained in a simultaneous search of both halves.

ZEDEfine must be invoked once for each DOFR, SUBS, DIST definition.

Example 1:

ZDEFINE DOFR 11 DIHE 44 CA 44 CB 44 CG 44 OD1

This defines the 11th degree of freedom as a dihedral involving atoms CA,

CB, CG, and OD1 of residue 44.

Example 2:

ZDEFine SUBStructure 2 sele resi 20 .around. 15 end -

SELE RESI 20 END

This defines the second substructure as containing all atoms within 15

angstroms of residue 20 and specifies that residue 20 will be rebuilt

in the searches.

Example 3:

ZDEFine DFCO 1 DOF 11 GTHAn -100 LTHAn 100

This defines the first internal coordinate constraint as being

applied to degree of freedom 11 (the dihedral angle as defined above),

with bounds of [-100,100] degrees.

-------------------------------------------------------------------------------

ZREAd

Reads in input conformer files. CONF reads in a conformer file from unit

RUNI and writes the "compressed" conformer file to unit WUNI. The conformer

file is compressed in the sense that there is no redundant information when the

file is read from start to finish--i.e. only the degrees of freedom that change

from one conformer to the next are written. This form of the file, which is

the form stored internally and used by the module, decreases space and memory

requirements and increases speed. ZREAd also sorts each conformer by degree of

freedom internally. ZREAd expects the first conformer of each subspace to be

"complete"--i.e. all its degrees of freedom must be present. Subsequent

conformers in the subspace may be present in compressed form.

The format of the conformer file is as follows (fortran format

I14,I14,I14,F14.7):

1 1 7 18.4857895

1 1 3 180.7483736

1 1 1 50.1098635

1 2 7 24.2836786

1 2 3 180.7483736

1 2 1 50.1098635

1 3 7 30.09877

1 3 3 180.168350

1 3 1 60.87635

2 4 8 64.27840

2 4 9 80.287635

2 4 11 17.981386

2 5 8 56.976233

2 5 9 80.287635

2 5 11 1.8923759

The first column gives the subspace number, the second column gives the

conformer number, the third column gives the degree of freedom, and the fourth

column gives the numerical value taken by the degree of freedom. This example

file has not been compressed. The compressed file would appear as follows:

1 1 1 50.1098635

1 1 3 180.7483736

1 1 7 18.4857895

1 2 7 24.2836786

1 3 1 60.8763500

1 3 3 180.1683500

1 3 7 30.0987700

2 4 8 64.2784000

2 4 9 80.2876350

2 4 11 17.9813860

2 5 8 56.9762330

2 5 11 1.8923759

Note that parts of conformers 2 and 5 have been omitted in the compressed file

because they contain redundant information.

By default, ZREAd expects the input file to have perfectly ordered (and

consecutive) conformer and subspace numbers, beginning with 1. This behavior

can be overridden with the MISSing and SSDisorder subcommand, respectively.

MISSing allows for "gaps" in conformer numbers (they still need to be ordered),

and SSDIsorder allows for disorder in the subspace numbers. This means that,

for example, subspace 2 can occur before subspace 1 in the file. However,

each subspace must be made up of consecutive input lines--i.e. subspaces cannot

be "split" in a given conformer file. ZREAd also expects degrees of freedom

not to occur in multiple subspaces. This can be overridden with the subcommand

REDUndant, which is necessary when subspaces overlap or when the same subspace

is defined twice (either with or without aliasing). If two consecutive

conformers in a conformer file are exactly the same, ZREAd will complain, but

it does not check the entire list for conformer redundancies. ZREAd expects

the first subspace in a file to be subspace 1; this again can be overridden

with the SSDIsorder subcommand.

If multiple conformer files are read in, each requires a separate ZREAd

CONFormer command, and the subspaces of the files will be renumbered

internally, so that they are consecutive. For example, if the last subspace of

the first file is 10, the first subspace of the second file will be called

subspace 11, regardless of the number appearing in the subspace column. In

general, if multiple conformer files are being read, the subspaces should be

well-ordered in all files--i.e. no "gaps" or inverted orders within each given

file. The SSDIsorder subcommand may not help in the case of multiple conformer

files with disordered subspace numbers.

-------------------------------------------------------------------------------

ZLOAd

"Loads" subspaces or constraints to be used in searches. This means the

specified subspaces or constraints are selected out of the sets of all possible

defined subspaces or constraints, and will be used in the searches.

If the "SUBS" subcommand is used, the selected subspace/substructure will be

used in the searches. A subspace/substructure must be loaded in order to be

searched. (Substructure/subspace aliases should also be loaded if they

are to be searched.) Note that if more than one substructure/subspace

is loaded, the "product" subspace/substructure--i.e. the one appearing

in the output conformer file--will generally be larger than each of the

"reactant" subspaces/substructures, since the product is the union of all

the reactant (loaded) subspaces/substructures.

The "NULL" subcommand allows for the loading of empty subspaces--i.e. ones

containing no conformers or ones for which no conformer file has been read in.

This is usefull in cases where, for example, a single subspace corresponds to

(the union of) 2 previously defined substructures. When it is used, the

"NULL" subcommand must occur as the first subcommand in the ZLOAd command.

If the "DIST" subcommand is used, the selected distance constraints will be

applied in the searches.

The "DFCOnstraints" subcommand is analogous to the "DIST" subcommand, except it

is used for loading the internal coordinate (DOF) constraints.

The CLEAr subcommand causes the previously loaded subspaces (or distance

constraints) to be unloaded prior to the parsing of any other subcommand in the

ZLOAd command.

-------------------------------------------------------------------------------

ZSPEcifications

This command causes the currently stored (user defined) search

specifications to be written to standard output.

-------------------------------------------------------------------------------

ZSEArch

Carries out N!/(N-n)!n! grid searches of the N loaded subspaces taken n at

a time, where n <= N. It eliminates conformers that are above specified

thresholds in energy, or outside of distance constraints, and can write

results to a product conformer file or a .dcd file (or both). The output

conformer file is formatted exactly as the input conformer file, except that,

in addition to the subspace, conformer, degree-of-freedom, and d.o.f.

numerical value information, the energies are also written in an additional

column to the right (in 1X,F19.7 fortran format). For convenience, the energy

of each conformer is written next to each of its component degrees of freedom.

If requested, the MSD's (mean square deviations from a target structure) are

written to a sixth column. If writing to a .dcd file is specified, all atoms

in the system are included.

TAKE {int} specifies the number of subspaces to be searched in

combination--i.e. the dimensionality of the grid ('n' in the expression above).

WCOM partially compresses the information in the output conformer file.

For each grid, only the first outputted conformer is written in its entirety;

the remaining conformers include only degrees of freedom that are being varied

in that grid. Since the ZREAd command requires that the first conformer be

"complete," and since the conformers are only accessed serially from the

start of the file, care should be taken when modifying a compressed conformer

output file prior to its use as an input file for a subsequent search. In

general, such modification is not recommended.

ECUT (real} and VCUT {real} are the fixed and variable energy cutoffs,

below which conformers will not be written to the output conformer file. If

both are specified, both cutoffs are used. ECUT is an absolute energy cutoff

value. VCUT is a tolerance above the running energy minimum and hence varies

over the course of the calculation. For example, ECUT 2000 VCUT 30 would

result in the exclusion of all conformers with energies > 2000 kcal/mol OR

>30 kcal/mol above the running minimum (but not necessarily the absolute

minimum).

MINA assigns the structure (main coordinate set) to the global minimum

after the search is completed.

WRUN the unit number to which the output conformer file is to be written.

MWRU is the write unit number to which the minimum-energy conformer file

is to be written.

TAG {int} is the numerical (integer) name given to the product subspace

and written in the first column of the output conformer file.

CFIX subcommand causes the non-bonded energy contributions of fixed-fixed

atom pairs not to be calculated (bonded energy contributions remain).

Fixed atoms are defined as ones that are not specified as moving for any

of the substructures included in a search. I.e. the moving atoms in a search

are taken as the union of the second atom selections of all the ZDEFINE

SUBStructure commands corresponding to the loaded substructures. The fixed

atoms are all the atoms in the system that are not taken as moving.

Since a significant fraction of the atoms included in the searches may not

be moving, the use of CFIX may speed up the calculations without affecting

the relative energies. Note that CFIX will also fix the atoms during

minimization.

MSD calculates the MSDs (mean squared deviations, or squared RMSDs) of the

conformers from the structure in the comparison coordinates. The MSD's are

calculated for all atoms in all the loaded substructures (union of all first

atom selections in the ZDEFine SUBStructure command). Least-squares-fit

reorientation is done prior to rmsd calculation unless the NOORientation

subcommand is also specified. The MSD subcommand currently is not compatible with

WCOMpression.

SPECifics subcommand causes the user-defined specifications that will

be used in the search to be written to standard output.

WDUN unit for writing out structures to .dcd ("trajectory") files.

NDSTeps total number of frames to be written to .dcd [default = 1000]

NOEN causes the energies not to be calculated. This is useful,

for example, when using only distance or internal coordinate constraints,

or when reading in a conformer file only for the purposes of writing out

the corresponding .dcd file.

SD {int} or CONJ {int} cause a minimization of the coordinates to be

carried out at each gridpoint in the search. The coordinates of all

atoms involved in the search (union of all loaded substructures) are minimized,

unless constraints are set prior to the minimization (e.g. CONS FIX can be

used as usual, outside of the Z module). Note that after

each minimization, the unminimized coordinates are restored before the next

point on the grid. This is necessary to preserve the internal coordinates that

are not being explicitly searched but are nontheless affected by minimization.

The non-bonded list is always updated at the start of the minimizations,

provided the update frequency (INBF) is > 0. The energies written to the

conformer file and the structures written to the .dcd file correspond to the

minimized coordinates. The assigned minimum-energy structure (which is

obtained with the MINA subcommand in the ZSEArch command) corresponds to the

unminimized coordinates.

-------------------------------------------------------------------------------

ZMIN

assigns the structure to the minimum indicated. If LOAD subcommand

specified, it assigns the structure to the minimum over all searches done

since the last ZLOAD command.

ZMOD Subcommand Description

-------------------------------------------------------------------------------

ZMOD

END

Enter (ZMOD) and exit (END) the Z module.

-------------------------------------------------------------------------------

ZMEMory

Allocates memory for the entire module. It and several subcommands must be

specified before any other ZMOD subcommands are given. NDOFs is the number of

degrees of freedom to be defined in the system; NSUBspaces is the number of

subspaces/substructures to be defined; NCONFormers is the total number of

conformers in all subspaces to be read in via conformer files; NVALues is the

cumulative length of all conformer files (total number of degree of freedom

values, one value per line) to be read in; NATOM is the total number of atoms

in all substructures (since atoms can occur in multiple substructures, this

number may exceed the total number of atoms in the system); CSIZe is the

maximum number of degrees of freedom that occur in any one conformer

(optional). NDIST is the number of distance constraints (required only

if distance constraints are being used). NDAToms is the total number of atoms

used in all of the distance constraints (required only for distance

constraints). NDFConstraints is the number of degree-of-freedom constraints

(required only for use of DOF constraints the degrees of freedom (DOFR),

the substructures (SUBS), distance constraints (DIST), and internal coordinate

constraints (DFCO) which must all be numbered serially from 1. The degrees

of freedom (DOFR) syntax is similar to that for editing the IC table

(see IC EDIT), and involves either bond distances (BOND), bond angles (ANGL),

or improper or proper dihedral angles (DIHE). The IC table should have been

filled "IC FILL" prior to the ZDEFine DOFR command. Importantly, when a degree

of freedom (DOFR subcommand) is thus defined, its initial value from the IC table

is stored and used as a default value when the subspace containing that degree

of freedom is included among the N subspaces in a search but is not one of

the n subspaces being searched on the current grid.

Although the degree-of-freedom definitions can be changed easily with the

ZDEFine DOFR command, for convenience, the design of the Z module is

intended to allow the user to define all the necessary degrees of freedom

initially, and then to perform all searches on the basis of that initial set of

definitions.

The MXLN subcommand can be used in parallel execution to increase memory associated

with the handling of data output

-------------------------------------------------------------------------------

ZDEFine

The substructure definition contains two atom selections: the first

defines the atoms that make up the substructure, and the second defines

the moving atoms--i.e. the atoms whose positions are to be initialized and

rebuilt during the searches. By default, the Cartesian coordinates are built

from the internal coordinates in the order of the atom numbers in the

substructure, lowest to highest. The REVErse subcommand causes the substructure

to be built up in the opposite sense, from higher atom number to lower. This

reversal is applied only to those substructures to which the subcommand is

assigned (and their aliases). The "REVErse" subcommand is often necessary, for

example, in building up loop structures from N-terminal and C-terminal halves.

(The alternative to explicitly defining a substructure is to define it

as an alias of another one by use of the subcommand "ALIAs {int}."

This is useful in combination with the ZCATegorize MINOR and ZSEARCh MINOR

commands to search the same subspace in two different regions.

See Searching Subspaces in Two Regions, below.)

The distance constraint definitions also contain two atom selections

each. Each constraint is applied to the distance between the centers of

geometry of the two selections. The distance constraint number

(serially ordered from 1), two atom selections, and upper and lower distance

bounds must be given for each distance constraint.

The internal coordinate or DOF constraint (DFCO) definitions require the

specification of the DOF constraint number as well as the integer corresponding

to the actual degree of freedom as defined in the ZDEFine DOF commands. The

upper and lower bounds for the constraints (in degrees) must also be specified.

The constraints are currently implemented for dihedral, improper, and bond

angles (not bond lengths). The bounds must be in the interval [-360,360]. This

feature is intended for applying constraints to degrees of freedom that are not

explicitly being searched. A good example occurs in loop searches, in which

both halves of the loop are being searched together for low-energy

combinations. The dihedral between the two searched halves of the loop is not

explicitly being searched (it doesn't exist in either half of the loop), but it

may need to be constrained in a simultaneous search of both halves.

ZEDEfine must be invoked once for each DOFR, SUBS, DIST definition.

Example 1:

ZDEFINE DOFR 11 DIHE 44 CA 44 CB 44 CG 44 OD1

This defines the 11th degree of freedom as a dihedral involving atoms CA,

CB, CG, and OD1 of residue 44.

Example 2:

ZDEFine SUBStructure 2 sele resi 20 .around. 15 end -

SELE RESI 20 END

This defines the second substructure as containing all atoms within 15

angstroms of residue 20 and specifies that residue 20 will be rebuilt

in the searches.

Example 3:

ZDEFine DFCO 1 DOF 11 GTHAn -100 LTHAn 100

This defines the first internal coordinate constraint as being

applied to degree of freedom 11 (the dihedral angle as defined above),

with bounds of [-100,100] degrees.

-------------------------------------------------------------------------------

ZREAd

Reads in input conformer files. CONF reads in a conformer file from unit

RUNI and writes the "compressed" conformer file to unit WUNI. The conformer

file is compressed in the sense that there is no redundant information when the

file is read from start to finish--i.e. only the degrees of freedom that change

from one conformer to the next are written. This form of the file, which is

the form stored internally and used by the module, decreases space and memory

requirements and increases speed. ZREAd also sorts each conformer by degree of

freedom internally. ZREAd expects the first conformer of each subspace to be

"complete"--i.e. all its degrees of freedom must be present. Subsequent

conformers in the subspace may be present in compressed form.

The format of the conformer file is as follows (fortran format

I14,I14,I14,F14.7):

1 1 7 18.4857895

1 1 3 180.7483736

1 1 1 50.1098635

1 2 7 24.2836786

1 2 3 180.7483736

1 2 1 50.1098635

1 3 7 30.09877

1 3 3 180.168350

1 3 1 60.87635

2 4 8 64.27840

2 4 9 80.287635

2 4 11 17.981386

2 5 8 56.976233

2 5 9 80.287635

2 5 11 1.8923759

The first column gives the subspace number, the second column gives the

conformer number, the third column gives the degree of freedom, and the fourth

column gives the numerical value taken by the degree of freedom. This example

file has not been compressed. The compressed file would appear as follows:

1 1 1 50.1098635

1 1 3 180.7483736

1 1 7 18.4857895

1 2 7 24.2836786

1 3 1 60.8763500

1 3 3 180.1683500

1 3 7 30.0987700

2 4 8 64.2784000

2 4 9 80.2876350

2 4 11 17.9813860

2 5 8 56.9762330

2 5 11 1.8923759

Note that parts of conformers 2 and 5 have been omitted in the compressed file

because they contain redundant information.

By default, ZREAd expects the input file to have perfectly ordered (and

consecutive) conformer and subspace numbers, beginning with 1. This behavior

can be overridden with the MISSing and SSDisorder subcommand, respectively.

MISSing allows for "gaps" in conformer numbers (they still need to be ordered),

and SSDIsorder allows for disorder in the subspace numbers. This means that,

for example, subspace 2 can occur before subspace 1 in the file. However,

each subspace must be made up of consecutive input lines--i.e. subspaces cannot

be "split" in a given conformer file. ZREAd also expects degrees of freedom

not to occur in multiple subspaces. This can be overridden with the subcommand

REDUndant, which is necessary when subspaces overlap or when the same subspace

is defined twice (either with or without aliasing). If two consecutive

conformers in a conformer file are exactly the same, ZREAd will complain, but

it does not check the entire list for conformer redundancies. ZREAd expects

the first subspace in a file to be subspace 1; this again can be overridden

with the SSDIsorder subcommand.

If multiple conformer files are read in, each requires a separate ZREAd

CONFormer command, and the subspaces of the files will be renumbered

internally, so that they are consecutive. For example, if the last subspace of

the first file is 10, the first subspace of the second file will be called

subspace 11, regardless of the number appearing in the subspace column. In

general, if multiple conformer files are being read, the subspaces should be

well-ordered in all files--i.e. no "gaps" or inverted orders within each given

file. The SSDIsorder subcommand may not help in the case of multiple conformer

files with disordered subspace numbers.

-------------------------------------------------------------------------------

ZLOAd

"Loads" subspaces or constraints to be used in searches. This means the

specified subspaces or constraints are selected out of the sets of all possible

defined subspaces or constraints, and will be used in the searches.

If the "SUBS" subcommand is used, the selected subspace/substructure will be

used in the searches. A subspace/substructure must be loaded in order to be

searched. (Substructure/subspace aliases should also be loaded if they

are to be searched.) Note that if more than one substructure/subspace

is loaded, the "product" subspace/substructure--i.e. the one appearing

in the output conformer file--will generally be larger than each of the

"reactant" subspaces/substructures, since the product is the union of all

the reactant (loaded) subspaces/substructures.

The "NULL" subcommand allows for the loading of empty subspaces--i.e. ones

containing no conformers or ones for which no conformer file has been read in.

This is usefull in cases where, for example, a single subspace corresponds to

(the union of) 2 previously defined substructures. When it is used, the

"NULL" subcommand must occur as the first subcommand in the ZLOAd command.

If the "DIST" subcommand is used, the selected distance constraints will be

applied in the searches.

The "DFCOnstraints" subcommand is analogous to the "DIST" subcommand, except it

is used for loading the internal coordinate (DOF) constraints.

The CLEAr subcommand causes the previously loaded subspaces (or distance

constraints) to be unloaded prior to the parsing of any other subcommand in the

ZLOAd command.

-------------------------------------------------------------------------------

ZSPEcifications

This command causes the currently stored (user defined) search

specifications to be written to standard output.

-------------------------------------------------------------------------------

ZSEArch

Carries out N!/(N-n)!n! grid searches of the N loaded subspaces taken n at

a time, where n <= N. It eliminates conformers that are above specified

thresholds in energy, or outside of distance constraints, and can write

results to a product conformer file or a .dcd file (or both). The output

conformer file is formatted exactly as the input conformer file, except that,

in addition to the subspace, conformer, degree-of-freedom, and d.o.f.

numerical value information, the energies are also written in an additional

column to the right (in 1X,F19.7 fortran format). For convenience, the energy

of each conformer is written next to each of its component degrees of freedom.

If requested, the MSD's (mean square deviations from a target structure) are

written to a sixth column. If writing to a .dcd file is specified, all atoms

in the system are included.

TAKE {int} specifies the number of subspaces to be searched in

combination--i.e. the dimensionality of the grid ('n' in the expression above).

WCOM partially compresses the information in the output conformer file.

For each grid, only the first outputted conformer is written in its entirety;

the remaining conformers include only degrees of freedom that are being varied

in that grid. Since the ZREAd command requires that the first conformer be

"complete," and since the conformers are only accessed serially from the

start of the file, care should be taken when modifying a compressed conformer

output file prior to its use as an input file for a subsequent search. In

general, such modification is not recommended.

ECUT (real} and VCUT {real} are the fixed and variable energy cutoffs,

below which conformers will not be written to the output conformer file. If

both are specified, both cutoffs are used. ECUT is an absolute energy cutoff

value. VCUT is a tolerance above the running energy minimum and hence varies

over the course of the calculation. For example, ECUT 2000 VCUT 30 would

result in the exclusion of all conformers with energies > 2000 kcal/mol OR

>30 kcal/mol above the running minimum (but not necessarily the absolute

minimum).

MINA assigns the structure (main coordinate set) to the global minimum

after the search is completed.

WRUN the unit number to which the output conformer file is to be written.

MWRU is the write unit number to which the minimum-energy conformer file

is to be written.

TAG {int} is the numerical (integer) name given to the product subspace

and written in the first column of the output conformer file.

CFIX subcommand causes the non-bonded energy contributions of fixed-fixed

atom pairs not to be calculated (bonded energy contributions remain).

Fixed atoms are defined as ones that are not specified as moving for any

of the substructures included in a search. I.e. the moving atoms in a search

are taken as the union of the second atom selections of all the ZDEFINE

SUBStructure commands corresponding to the loaded substructures. The fixed

atoms are all the atoms in the system that are not taken as moving.

Since a significant fraction of the atoms included in the searches may not

be moving, the use of CFIX may speed up the calculations without affecting

the relative energies. Note that CFIX will also fix the atoms during

minimization.

MSD calculates the MSDs (mean squared deviations, or squared RMSDs) of the

conformers from the structure in the comparison coordinates. The MSD's are

calculated for all atoms in all the loaded substructures (union of all first

atom selections in the ZDEFine SUBStructure command). Least-squares-fit

reorientation is done prior to rmsd calculation unless the NOORientation

subcommand is also specified. The MSD subcommand currently is not compatible with

WCOMpression.

SPECifics subcommand causes the user-defined specifications that will

be used in the search to be written to standard output.

WDUN unit for writing out structures to .dcd ("trajectory") files.

NDSTeps total number of frames to be written to .dcd [default = 1000]

NOEN causes the energies not to be calculated. This is useful,

for example, when using only distance or internal coordinate constraints,

or when reading in a conformer file only for the purposes of writing out

the corresponding .dcd file.

SD {int} or CONJ {int} cause a minimization of the coordinates to be

carried out at each gridpoint in the search. The coordinates of all

atoms involved in the search (union of all loaded substructures) are minimized,

unless constraints are set prior to the minimization (e.g. CONS FIX can be

used as usual, outside of the Z module). Note that after

each minimization, the unminimized coordinates are restored before the next

point on the grid. This is necessary to preserve the internal coordinates that

are not being explicitly searched but are nontheless affected by minimization.

The non-bonded list is always updated at the start of the minimizations,

provided the update frequency (INBF) is > 0. The energies written to the

conformer file and the structures written to the .dcd file correspond to the

minimized coordinates. The assigned minimum-energy structure (which is

obtained with the MINA subcommand in the ZSEArch command) corresponds to the

unminimized coordinates.

-------------------------------------------------------------------------------

ZMIN

assigns the structure to the minimum indicated. If LOAD subcommand

specified, it assigns the structure to the minimum over all searches done

since the last ZLOAD command.

Top

ZMOD Command Usage Examples

ZMOD !enter module

ZMEMOry NDOF 100 NSUBSPACE 20 NATOM 25000 NCONF 2000 NVAL 10000 !allocate memory

ZDEFINE DOFR 1 DIHE 10 C 11 N 11 CA 11 C

ZDEFINE DOFR 2 DIHE 11 N 11 CA 11 C 12 N

ZDEFINE DOFR 3 DIHE 11 C 12 N 12 CA 12 C

ZDEFINE DOFR 4 DIHE 12 N 12 CA 12 C 13 N

ZDEFINE DOFR 5 DIHE 29 C 30 N 30 CA 30 C

ZDEFINE DOFR 6 DIHE 30 N 30 CA 30 C 31 N

ZDEFINE DOFR 7 DIHE 30 C 31 N 31 CA 31 C

ZDEFINE DOFR 8 DIHE 31 N 31 CA 31 C 32 N

ZDEFINE DOFR 9 DIHE 35 C 36 N 36 CA 36 C

ZDEFINE DOFR 10 DIHE 36 N 36 CA 36 C 37 N

ZDEFine SUBStructure 1 SELE ALL END SELE IRES 1:13 END

ZDEFine SUBStructure 2 SELE ALL END SELE IRES 1:32 END

ZDEFine SUBStructure 3 SELE ALL END SELE IRES 1:38 END

ZDEFine SUBStructure 4 SELE ALL END SELE IRES 1:50 END

open unit 12 write card name echodata

open unit 10 read card name short.conf !conformer file

ZREAD REDU CONF RUNI 10 WUNI 12 !we are allowing redundancy of dofs in the

!conformer file

END ! exit the Z module

!other charmm commands here

ENERGY

MINIMIZE SD

ZMOD !reenter Z module

ZLOAD SUBS CLEAR 2 3 4 !load 3 out of 4 defined subspaces

open unit 15 write card name ener.file

!specify searches that take 2 subspaces at a time

!write to unit 15, assign the minimum to the main coordinate

!set after the search, set product subspace tag to one (for output),

!save (and write) only the conformers within 500 kcal/mol of the running

!minimum energy, write search specifications to standard output

ZSEArch TAKE 2 WRUN 15 MINAssign TAG 1 VCUT 500 SPEC

close unit 15

END !exit Z module

!other charmm input:

COOR RMS ORIENT SELE ALL END

OPEN UNIT 10 WRITE CARD NAME crd/final.crd

WRITE COOR CARD UNIT 10

CLOSE UNIT 10

-------------------------------------------------------------------------------

ZSET

Finalizes or 'sets" the input data in preparation for a search. In parallel

execution, the subcommand also triggers communication of the data to all nodes.

-------------------------------------------------------------------------------

ZRANdom

Randomly selects conformers in one or more subspaces from the set that

has been read in. The SUBS subcommand allows specification of the subspaces

to be included in the random selection and actually triggers the selecion.

It can be followed either by 1) pairs of integers--subspace number followed by the

number of conformers to be selected; or 2) the ALLSubspace subcommand, which

specifies that all subspaces are to be included in the selection, followed

by a single integer, which is the number of conformers to be selected in

each subspace. The subspaces not included in the selection are left as they

are. The SEED (positive integer) subcommand sets the seed for the random

conformer selection. It must be set prior to (in the same ZRANdom command as)

the SUBSpace subcommand. WUNIt is the unit number for writing out the selected

conformers. ECUT and VCUT are fixed and variable energy cutoffs, respectively,

as described under ZSEArch.

examples

ZRAN SEED 189876500

ZRAN SUBS 1 3 2 10 3 15 4 20

--------------

ZRANDOM SEED 189876500 SUBS ALLSubspaces 30 WUNI 19 ECUT -2200

In the top example, the random seed is set, and then random selections of

3, 10, 15, and 20 conformers are invoked for subspaces 1 through 4, respectively.

In the second example, random selections of 30 conformers are are invoked for

all subspaces, with the specified seed and an energy cutoff of -2200 kcal/mol,

writing the output to unit 19

ZFIL

Filters the conformers that have been read in by energy; can set different

energy cutoffs for different subspaces. The LECUt subcommand specifies

the subspaces and their respective fixed energy cutoffs. The LVCUt subcommand

specifies energy bands (tolerance above minimum) local to each subspace,

whereas the VCUT and ECUT subcommands specify global cutoffs, as above.

example

ZFILter LVCUt 5 LECUt 1 50 2 20 3 10 END

Here the fixed energy cutoffs specified are 50, 20, and 10 kcal/mol for

subspaces 1 to 3, respectively. There is, in addition, a cutoff of

5 kcal/mol above the energy minimum for each subspace.

ZMOD Command Usage Examples

ZMOD !enter module

ZMEMOry NDOF 100 NSUBSPACE 20 NATOM 25000 NCONF 2000 NVAL 10000 !allocate memory

ZDEFINE DOFR 1 DIHE 10 C 11 N 11 CA 11 C

ZDEFINE DOFR 2 DIHE 11 N 11 CA 11 C 12 N

ZDEFINE DOFR 3 DIHE 11 C 12 N 12 CA 12 C

ZDEFINE DOFR 4 DIHE 12 N 12 CA 12 C 13 N

ZDEFINE DOFR 5 DIHE 29 C 30 N 30 CA 30 C

ZDEFINE DOFR 6 DIHE 30 N 30 CA 30 C 31 N

ZDEFINE DOFR 7 DIHE 30 C 31 N 31 CA 31 C

ZDEFINE DOFR 8 DIHE 31 N 31 CA 31 C 32 N

ZDEFINE DOFR 9 DIHE 35 C 36 N 36 CA 36 C

ZDEFINE DOFR 10 DIHE 36 N 36 CA 36 C 37 N

ZDEFine SUBStructure 1 SELE ALL END SELE IRES 1:13 END

ZDEFine SUBStructure 2 SELE ALL END SELE IRES 1:32 END

ZDEFine SUBStructure 3 SELE ALL END SELE IRES 1:38 END

ZDEFine SUBStructure 4 SELE ALL END SELE IRES 1:50 END

open unit 12 write card name echodata

open unit 10 read card name short.conf !conformer file

ZREAD REDU CONF RUNI 10 WUNI 12 !we are allowing redundancy of dofs in the

!conformer file

END ! exit the Z module

!other charmm commands here

ENERGY

MINIMIZE SD

ZMOD !reenter Z module

ZLOAD SUBS CLEAR 2 3 4 !load 3 out of 4 defined subspaces

open unit 15 write card name ener.file

!specify searches that take 2 subspaces at a time

!write to unit 15, assign the minimum to the main coordinate

!set after the search, set product subspace tag to one (for output),

!save (and write) only the conformers within 500 kcal/mol of the running

!minimum energy, write search specifications to standard output

ZSEArch TAKE 2 WRUN 15 MINAssign TAG 1 VCUT 500 SPEC

close unit 15

END !exit Z module

!other charmm input:

COOR RMS ORIENT SELE ALL END

OPEN UNIT 10 WRITE CARD NAME crd/final.crd

WRITE COOR CARD UNIT 10

CLOSE UNIT 10

-------------------------------------------------------------------------------

ZSET

Finalizes or 'sets" the input data in preparation for a search. In parallel

execution, the subcommand also triggers communication of the data to all nodes.

-------------------------------------------------------------------------------

ZRANdom

Randomly selects conformers in one or more subspaces from the set that

has been read in. The SUBS subcommand allows specification of the subspaces

to be included in the random selection and actually triggers the selecion.

It can be followed either by 1) pairs of integers--subspace number followed by the

number of conformers to be selected; or 2) the ALLSubspace subcommand, which

specifies that all subspaces are to be included in the selection, followed

by a single integer, which is the number of conformers to be selected in

each subspace. The subspaces not included in the selection are left as they

are. The SEED (positive integer) subcommand sets the seed for the random

conformer selection. It must be set prior to (in the same ZRANdom command as)

the SUBSpace subcommand. WUNIt is the unit number for writing out the selected

conformers. ECUT and VCUT are fixed and variable energy cutoffs, respectively,

as described under ZSEArch.

examples

ZRAN SEED 189876500

ZRAN SUBS 1 3 2 10 3 15 4 20

--------------

ZRANDOM SEED 189876500 SUBS ALLSubspaces 30 WUNI 19 ECUT -2200

In the top example, the random seed is set, and then random selections of

3, 10, 15, and 20 conformers are invoked for subspaces 1 through 4, respectively.

In the second example, random selections of 30 conformers are are invoked for

all subspaces, with the specified seed and an energy cutoff of -2200 kcal/mol,

writing the output to unit 19

ZFIL

Filters the conformers that have been read in by energy; can set different

energy cutoffs for different subspaces. The LECUt subcommand specifies

the subspaces and their respective fixed energy cutoffs. The LVCUt subcommand

specifies energy bands (tolerance above minimum) local to each subspace,

whereas the VCUT and ECUT subcommands specify global cutoffs, as above.

example

ZFILter LVCUt 5 LECUt 1 50 2 20 3 10 END

Here the fixed energy cutoffs specified are 50, 20, and 10 kcal/mol for

subspaces 1 to 3, respectively. There is, in addition, a cutoff of

5 kcal/mol above the energy minimum for each subspace.

Top

More Complex Searches: Searching Subspaces in Two Regions

In some cases, the user may want to be able to search the same

conformational subspace in two different regions in a series of grids. Take,

for example, the case of 3 rigid helices for which the optimal packing

arrangement is sought. The most efficient search algorithm may be one in

which each helix is allowed to sample a large region of conformational space,

while the other two helices make local adjustments. Hence, each helix would

have two defined regions: one for the large changes and one for the local

adjustments--i.e. a "major" and a "minor" region. As helix A was searched in

its major region, helices B and C would be searched in their minor regions, and

likewise for the other combinations.

Rather than introduce a "region" formalism into the structure of the

Z module--i.e. having each subspace be composed of multiple regions--which

would be complicated for both users and developers, the decision was made to

allow subspaces to have aliases. The alias of a subspace has exactly the same

degrees of freedom and atomic substructure, but it is called separately and can

be assigned different conformations from its primary subspace counterpart

through the conformer file(s). The CATEgorize MINOr command is necessary to

categorize the aliased subspace as "minor", or secondary, so that it is treated

as such in the ZSEARch command. The "MINOR {int}" subcommand must be used in the

ZSEArch command to indicate how many minor subspaces or regions are to be

searched at a time.

ZDEFine SUBSPACE {int} ALIAS {int} is used as an alternative to explicitly

defining an atomic substructure. The integer after ALIAS specifies the number

of the primary subspace to which the alias corresponds. Aliasing is necessary

when searching two regions of the same subspace (i.e. a subspace and its alias)

in a set of searches, because it tells the ZSEArch command that the two loaded

subspaces correspond. This allows the Z module to exclude search grids in

which the same subspace effectivley appears more than once. Without aliasing,

subspaces are combined in searches without regard to whether they are the same

or not, so that results may be redundant or incomplete. The atom selections

and REVErsal specifications are not necessary (and not allowed) when ALIAsing

a subspace.

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Syntax for additional commands in multiple-region searches:

ZCATegorize MINOr CLEAR NONE {int1 int2 int3 ... }

ZSEArch MINO {int} RESS

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Description of additional commands

ZCATegorize

Categorizes a subspace, effectively creating a different search region for

the space. Currently, only one alternative region can be searched for a given

subspace, which is assigned the category (subcommand) "MINOr." The subcommand

"minor" indicates that the subspace is to be included in the set of "MINOr"

or secondary regions that are to be searched by the ZSEARch command (it implies

nothing about size). A set of integers must be specified which refer to the

numbers of the subspaces being categorized as minor. The CLEAR or NONE

subcommands clear any previous categorizations of subspaces as minor.

-------------------------------------------------------------------------------

ZSEARCH MINOR {int} RESS

MINOr {int} specifies the number of subspaces, out of TAKE searched

subspaces, that should be searched in their "minor" or alternative regions

[default=0].,

The RESS ("REpeat SubSpace") subcommand allows multiple versions of the same

subspace, as defined by the ZDEFine ALIAS command, to be searched at the same

time (i.e. on the same search grid). This is not generally recommended and the

user employs this subcommand at his own risk.

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Example

An example of a search using multiple subspace regions, modified from

an example above

ZMOD !enter module

ZMEMOry NDOF 100 NSUBSPACE 20 NATOM 25000 NCONF 2000 NVAL 10000 !allocate memory

ZDEFINE DOFR 1 DIHE 10 C 11 N 11 CA 11 C

ZDEFINE DOFR 2 DIHE 11 N 11 CA 11 C 12 N

ZDEFINE DOFR 3 DIHE 11 C 12 N 12 CA 12 C

ZDEFINE DOFR 4 DIHE 12 N 12 CA 12 C 13 N

ZDEFINE DOFR 5 DIHE 29 C 30 N 30 CA 30 C

ZDEFINE DOFR 6 DIHE 30 N 30 CA 30 C 31 N

ZDEFINE DOFR 7 DIHE 30 C 31 N 31 CA 31 C

ZDEFINE DOFR 8 DIHE 31 N 31 CA 31 C 32 N

ZDEFINE DOFR 9 DIHE 35 C 36 N 36 CA 36 C

ZDEFINE DOFR 10 DIHE 36 N 36 CA 36 C 37 N

ZDEFine SUBStructure 1 SELE ALL END SELE IRES 1:13 END

ZDEFine SUBStructure 2 SELE ALL END SELE IRES 1:32 END

ZDEFine SUBStructure 3 SELE ALL END SELE IRES 1:38 END

ZDEFine SUBStructure 4 SELE ALL END SELE IRES 1:50 END

ZDEFine SUBStructure 5 ALIAs 1 ! 5 is same as 1 !***************

ZDEFine SUBStructure 6 ALIAs 2 ! 6 is same as 2 !***************

ZCAT CLEAR MINOR 5 6 ! categorizing 5 and 6 as minor subspaces (regions) !***

open unit 12 write card name echodata

open unit 10 read card name short.2.conf !conformer file, now contains

!conformers for subspaces 5 and 6 also

ZREAD REDU CONF RUNI 10 WUNI 12 ! allowing redundancy of dofs in conformer file

END ! exit the Z module

!other charmm input

ENERGY

MINIMIZE SD

ZMOD !reenter Z module

ZLOAD SUBS CLEAR 2 3 4 5 6 !load 5 out of 6 defined subspaces !***********

open unit 15 write card name ener.file

!specify searches that take 3 subspaces at a time, one of which is searched

!in its minor region, write to unit 15, assign the minimum to the main

!coordinate set after the search, set product subspace tag to one (for output),

!save (and write) only the conformers within 500 kcal/mol of the running

!minimum energy, write search specifications to standard output

!include minor subcommand *****************

ZSEArch TAKE 3 MINO 1 WRUN 15 MINAssign TAG 1 VCUT 500 SPEC !***************

close unit 15

END !exit Z module

!other charmm input:

COOR RMS ORIENT SELE ALL END

OPEN UNIT 10 WRITE CARD NAME crd/final.crd

WRITE COOR CARD UNIT 10

CLOSE UNIT 10

More Complex Searches: Searching Subspaces in Two Regions

In some cases, the user may want to be able to search the same

conformational subspace in two different regions in a series of grids. Take,

for example, the case of 3 rigid helices for which the optimal packing

arrangement is sought. The most efficient search algorithm may be one in

which each helix is allowed to sample a large region of conformational space,

while the other two helices make local adjustments. Hence, each helix would

have two defined regions: one for the large changes and one for the local

adjustments--i.e. a "major" and a "minor" region. As helix A was searched in

its major region, helices B and C would be searched in their minor regions, and

likewise for the other combinations.

Rather than introduce a "region" formalism into the structure of the

Z module--i.e. having each subspace be composed of multiple regions--which

would be complicated for both users and developers, the decision was made to

allow subspaces to have aliases. The alias of a subspace has exactly the same

degrees of freedom and atomic substructure, but it is called separately and can

be assigned different conformations from its primary subspace counterpart

through the conformer file(s). The CATEgorize MINOr command is necessary to

categorize the aliased subspace as "minor", or secondary, so that it is treated

as such in the ZSEARch command. The "MINOR {int}" subcommand must be used in the

ZSEArch command to indicate how many minor subspaces or regions are to be

searched at a time.

ZDEFine SUBSPACE {int} ALIAS {int} is used as an alternative to explicitly

defining an atomic substructure. The integer after ALIAS specifies the number

of the primary subspace to which the alias corresponds. Aliasing is necessary

when searching two regions of the same subspace (i.e. a subspace and its alias)

in a set of searches, because it tells the ZSEArch command that the two loaded

subspaces correspond. This allows the Z module to exclude search grids in

which the same subspace effectivley appears more than once. Without aliasing,

subspaces are combined in searches without regard to whether they are the same

or not, so that results may be redundant or incomplete. The atom selections

and REVErsal specifications are not necessary (and not allowed) when ALIAsing

a subspace.

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Syntax for additional commands in multiple-region searches:

ZCATegorize MINOr CLEAR NONE {int1 int2 int3 ... }

ZSEArch MINO {int} RESS

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Description of additional commands

ZCATegorize

Categorizes a subspace, effectively creating a different search region for

the space. Currently, only one alternative region can be searched for a given

subspace, which is assigned the category (subcommand) "MINOr." The subcommand

"minor" indicates that the subspace is to be included in the set of "MINOr"

or secondary regions that are to be searched by the ZSEARch command (it implies

nothing about size). A set of integers must be specified which refer to the

numbers of the subspaces being categorized as minor. The CLEAR or NONE

subcommands clear any previous categorizations of subspaces as minor.

-------------------------------------------------------------------------------

ZSEARCH MINOR {int} RESS

MINOr {int} specifies the number of subspaces, out of TAKE searched

subspaces, that should be searched in their "minor" or alternative regions

[default=0].,

The RESS ("REpeat SubSpace") subcommand allows multiple versions of the same

subspace, as defined by the ZDEFine ALIAS command, to be searched at the same

time (i.e. on the same search grid). This is not generally recommended and the

user employs this subcommand at his own risk.

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Example

An example of a search using multiple subspace regions, modified from

an example above

ZMOD !enter module

ZMEMOry NDOF 100 NSUBSPACE 20 NATOM 25000 NCONF 2000 NVAL 10000 !allocate memory

ZDEFINE DOFR 1 DIHE 10 C 11 N 11 CA 11 C

ZDEFINE DOFR 2 DIHE 11 N 11 CA 11 C 12 N

ZDEFINE DOFR 3 DIHE 11 C 12 N 12 CA 12 C

ZDEFINE DOFR 4 DIHE 12 N 12 CA 12 C 13 N

ZDEFINE DOFR 5 DIHE 29 C 30 N 30 CA 30 C

ZDEFINE DOFR 6 DIHE 30 N 30 CA 30 C 31 N

ZDEFINE DOFR 7 DIHE 30 C 31 N 31 CA 31 C

ZDEFINE DOFR 8 DIHE 31 N 31 CA 31 C 32 N

ZDEFINE DOFR 9 DIHE 35 C 36 N 36 CA 36 C

ZDEFINE DOFR 10 DIHE 36 N 36 CA 36 C 37 N

ZDEFine SUBStructure 1 SELE ALL END SELE IRES 1:13 END

ZDEFine SUBStructure 2 SELE ALL END SELE IRES 1:32 END

ZDEFine SUBStructure 3 SELE ALL END SELE IRES 1:38 END

ZDEFine SUBStructure 4 SELE ALL END SELE IRES 1:50 END

ZDEFine SUBStructure 5 ALIAs 1 ! 5 is same as 1 !***************

ZDEFine SUBStructure 6 ALIAs 2 ! 6 is same as 2 !***************

ZCAT CLEAR MINOR 5 6 ! categorizing 5 and 6 as minor subspaces (regions) !***

open unit 12 write card name echodata

open unit 10 read card name short.2.conf !conformer file, now contains

!conformers for subspaces 5 and 6 also

ZREAD REDU CONF RUNI 10 WUNI 12 ! allowing redundancy of dofs in conformer file

END ! exit the Z module

!other charmm input

ENERGY

MINIMIZE SD

ZMOD !reenter Z module

ZLOAD SUBS CLEAR 2 3 4 5 6 !load 5 out of 6 defined subspaces !***********

open unit 15 write card name ener.file

!specify searches that take 3 subspaces at a time, one of which is searched

!in its minor region, write to unit 15, assign the minimum to the main

!coordinate set after the search, set product subspace tag to one (for output),

!save (and write) only the conformers within 500 kcal/mol of the running

!minimum energy, write search specifications to standard output

!include minor subcommand *****************

ZSEArch TAKE 3 MINO 1 WRUN 15 MINAssign TAG 1 VCUT 500 SPEC !***************

close unit 15

END !exit Z module

!other charmm input:

COOR RMS ORIENT SELE ALL END

OPEN UNIT 10 WRITE CARD NAME crd/final.crd

WRITE COOR CARD UNIT 10

CLOSE UNIT 10