NAME

mkchaindes - generate a descriptor for a collection of identical spheres

SYNOPSIS

mkchaindes [ options ] -db bindes -n N_u

DESCRIPTION

Generate a binary descriptor bindes of N_u units. A unit may represent a single atom or a large number of atoms. For example, in the reduced representation model of DNA each unit may represent an entire base pair or as many as 10 base pairs. Each unit will be represented in the atomic model by a single atom. Each atom is identical to the next; there is only one type of atom in the system and therefore only one set of physico-chemical properties. Extra atomic types may be introduced for some options but these atoms will be excluded from any interaction with the standard atoms. The atoms may be free, i.e., not bonded to other atoms. The atoms may also be connected into a chain where atom 1 is bonded to atom 2 which in turn is bonded to atom 3 and so on until atom N_atom -1 is bonded to atom N_atom. The conformation of the chain may be restricted further by imposing angle constraints in which atoms 1,2,3 are constrained to a specific angle and so are atoms 2,3,4 and so on to the last triplet N_atom -2,N_atom-1,N_atom. The conformation may be restricted even further by imposing a torsional constraint in which atoms 1,2,3,4 are constrained to a set of allowable dihedral angles and so are atoms 2,3,4,5 and so on to the last quadruplet N_atom -3,N_atom -2,N_atom-1,N_atom. Finally, the chain may be closed into a circle where atom N_atom is bonded to atom 1.

When no options are specified a very simple descriptor is generated in which there are no interatomic interactions of any kind. Such a descriptor is of very little use in simulations.

The options are of three types and are explained in the following table. Options that act as "on" switches are written on the command line on their own without an accompanying value. These options are marked as type A. Type B options are specified on the command line as keyword-value pairs, the option keyword must be immediately followed by an appropriate value. If a type B option is specified more than once, all previous specifications are overwritten and only the last value remains. Type C options are like type B options but each specification fills an array from the top down; the first occurrence of a type C option specifies the value of the first element of the appropriate array, the second specifies the value of the second element of the array and so on. All options have preset values but these are rarely appropriate.

Option	Type	Preset	Units	Purpose
-note	C	.	.	Every line of note is collected in the order of occurrence and written to the descriptor. Protect each line from shell interpretation by enclosing them in quotes.
-atomname	C	UNIT,NONE	.	Names of the atoms. The first name is that of the chain atom.
-residname	C	CHAIN,CENTR	.	Names of the residues. The first name is that of the entire chain.
-mass	C	1,1	amu	Atomic masses, the first is for the chain atom.
-bond	A	[off]	.	Connect the atoms into a chain. Do not specify together with -morse.
-kbond	B	1	kcal mol-1 Å-2	Force constant for the bond term.
-bond0	B	1	Å	Equilibrium bond length.
-morse	A	[off]	.	Connect the atoms into a chain using the morse bond. Do not specify together with -bond.
-morseE	B	1	kcal mol-1	The base energy in the morse bond term.
-morseA	B	1	Å-1	This controls the width of the potential well.
-morseD	B	1	Å	Equilibrium bond length.
-angle	A	[off]	.	Connect the chain atoms by angle constraints. This will also turn on -bond provided -morse is not specified.
-kangl	B	1	kcal mol-1 radian-2	Force constant for the angle term.
-angl0	B	60	degree	Equilibrium bond angle
-torsion	A	[off]	.	Connect the chain atoms by torsion constraints. This will also turn on -angle. Do not specify this as well as -improper.
-period	B	3	.	Periodicity of the torsion. Must be an integer 1 to 6.
-ktors	B	1	kcal mol-1	Maximum energy in the torsion term
-phase	B	-1	.	Phase of the torsion energy term. This is usually 1 or -1 but any number can be specified.
-improper	A	[off]	.	Connect the chain atoms with improper torsions. This will turn on -angle as well. Do not specify this with -torsion.
-kitor	B	1	kcal mol-1 radian-2	Force constant for the improper torsion.
-itor0	B	36	degree	Equilibrium torsion angle.
-nonbond	A	[off]	.	Write a non bond exclusion term to the descriptor. Do not specify this together with -vanderwaals.
-nbexclude	B	0	.	Number of closely bonded atoms to exclude from this interaction.
-nbpower	B	2	.	The power to which the distance will be raised.
-nbcutoff	B	1.25	.	Cutoff ratio for the contact list. Must be greater than 1.
-nbsize	C	1,1	Å	Non bond contact distance or volume exclusion diameter.
-nbforce	C	1,0	kcal mol-1 Å-2	Force constant for the non-bond term
-vanderwaals	A	[off]	.	Write the van der Waals exclusion record to the descriptor. The function is trimmed with the switching function. Must not be specified together with -nonbond.
-vdwexclude	B	0	.	Number of closely bonded atoms to exclude from this interaction.
-vdwstart	B	10	Å	The distance at which the trimming starts.
-vdwstop	B	12.5	Å	... and finishes.
-vdwcutoff	B	15	Å	Atom pairs within this distance are gathered in the non-bond list.
-vdwA	C	1,1	kcal mol-1 Å-12	van der Waals constant for the 12-th power term.
-vdwB	C	0.1,0.1	kcal mol-1 Å-6	van der Waals constant for the 6-th power term.
-closed	A	[off]	.	Connect the two ends of the chain into a closed circle. This adds a bond (if -bond specified) or morse bond (if -morse specified), two angles (if -angle specified) and three torsions (if -torsion or -improper specified).
-sphere	A	[off]	.	Enclose the chain atoms in a sphere using NOE constraints. This introduces one atom that is excluded from all interactions with the chain atoms except for this constraint.
-SPHERE	C	.	.	Identical to the previous option except that only the specified nunber of atoms will be enclosed. If specified once, units number one to the specified number is enclosed. If specified twice the units between the two specified numbers (inclusive) are enclosed. It is an error to specify this more than twice.
-noepower	B	2	.	The power to which the distance is raised.
-noeklow	B	0	kcal mol-1 Å-2	Force constant at the inner barrier
-noedlow	B	0	Å	Inner barrier distance. The atoms are constrained to be outside this radius.
-noekhigh	B	1	kcal mol-1 Å-2	Force constant at the outer barrier.
-noedhigh	B	1	Å	Outer barrier distance. The atoms are constrained to be inside this radius.
-box	A	[off]	.	Enclose the chain atoms within a box centered on the origin of dimensions specified as follows...
-A	B	1	Å	The length of the box along the x'-axis
-B	B	1	Å	The length of the box along the y'-axis
-C	B	1	Å	The length of the box along the z'-axis
-alpha	B	90	degree	The angle between the y' and z' axes
-beta	B	90	degree	The angle between the x' and z' axes
-gamma	B	90	degree	The angle between the x' and y' axes
-Emax	B	0.59617	kcal mol-1	The energy barrier. The preset value is kT at 300K.
-lock	C	.	.	Add the named atom to the first lock set. There can be only one lock set.
-simple	A	.	.	Generate a very simple descriptor of a chain connected only by bonds.
-dnaball	B	.	Å	Generate a descriptor for the DNA packing problem.

If -note is not specified, a single line is created anyway and written to the descriptor. This merely contains the name of the person who created the descriptor and the date on which the descriptor is written.

The chain atoms are always of atom type 1 belonging to residue type 1. Special atoms may be introduced. For example -sphere introduces an atom type that is not involved in any interaction except for the spherical enclosure constraint. The type C options (-atomname -residname -mass -nbsize -nbforce -vdwA -vdwB) allow values to be set for each atom type. In most cases, the settings for the special atom types are just dummy values; they may be required but are not used in actual calculations.

Setting one of the torsion terms (-improper or -torsion) will also set -angle and setting -angle also sets -bond (unless -morse is specified). It is not possible to have a chain with torsional constraint but no bonds for instance. Some terms are incompatible with another; setting one precludes the other. The mutually exclusive pairs are -improper and -torsion, -bond and -morse, -nonbond and -vanderwaals.

The last two options are shortcuts to creating descriptors for specific models:

Selecting -simple is equivalent to specifying -bond -mass 300 -kbond 0.23922 -bond0 6.1. This is a simple reduced representation model of a RNA chain in which each unit represents a base of the RNA. This is the same result obtained from the first version of this program.

Specifying -dnaball D_sphere is equivalent to specifying -angl -nbnb -sphere -kbond 50.6766 -bond0 34 -kangl 3.92323 -angl0 180 -noepower 2 -noeklow 0 -noedlow 0 -noekhigh 50.6766 -noedhigh D_sphere -mass 1000 -nbsize 30 -nbforce 60.6766 -nbexclude 1 -nbpower 2. This is a model of DNA where each unit represents 10 base pairs and the bases are enclosed in a sphere of diameter D_sphere. Note that the units are bonded 34Å apart while each unit has a non-bond diameter of 30Å.; hence the nearest atom is excluded from non-bond consideration. You can override the values set by -dnaball and add other values by specifying them after this option. However, it is not possible to reverse the -sphere setting.

Since there are so many options it may be better to write a script containing all the options. The script can be proof-read and corrected before actual execution. You can write the command over many lines provided the appropriate line break character (backslash in UNIX) is used. A self-explanatory example is shown below.

# Sample Script to run mkchaindes with many options   mkchaindes -n 360 -db circulardna.ds \ -note 'Model of a 360 base pair circular DNA. Each base pair is represented by an atom which' \ -note 'is on the alternate sides of the base plane which is assumed to be 10A wide. This' \ -note 'traces out a zig-zag path which spirals in imitation of the DNA helix. The dimensions' \ -note 'are extracted from a real helix of zero roll and tilt and twist of 36 degrees.' \ \ -atomname SIDE \ -residname DNA \ -mass 729 \ -improper \ -nonbond \ -closed \ -kbond 50.7 -bond0 10.1 \ -kangl 43.7 -angl0 52.8 \ -kitor 63.5 -itor0 -92 \ -nbpower 6 \ -nbsize 10 \ -nbforce 596.3 \ -nbexclude 3 \ \ -note 'Descriptor created: RT, UAB, Sept. 17, 1998.'

Note that although the note is given in two separate sections, four lines at the start of the script and a solitary line at the end, all five lines will appear together as a single note record in the descriptor.

EXAMPLES

mkchaindes -vanderwaals -vdwA 0.59617 -vdwB 1.1923 -box -A 100 -B 100 -C 100 -db boxofballs.ds -vdwstart 22.5 -vdwstop 25 -vdwcutoff 30 -n 500

Generate a binary descriptor boxofballs.ds for 500 atoms with only van der Waals interaction. The van der Waals constants A and B are specified to have values of kT (0.59617 kcal mol^-1 Å^-12) and 2kT (1.1923 kcal mol^-1 Å^-6) respectively which corresponds to a van der Waals radius of 1Å and a minimum energy of -kT. A rectangular box of 100Å by 100Å by 100Å is specified which would hopefully prevent the atoms from evaporating during simulation. The trimming is specified to start at 22.5Å and finishes at 25Å. The cutoff distance is accordingly lengthened to 30Å.

FILES

A temporary file containing the text descriptor is created which is then converted to binary. If the conversion is successful, the temporary file is automatically removed. Otherwise it will remain for inspection. The name of the file is mkchaindes?????? where the last six characters are digits generated at random.

SEE ALSO

mkchainarc, des, The descriptor file format.

DIAGNOSTICS

The program will not proceed if the file specified after the -db option already exists. A new file name must be specified or the existing file must be removed first.

BUGS

The -vanderwaals and -closed options do not work properly together. The exclusion list for the van der Waals term will be generated for an open chain only.

NOTES

Creating a descriptor is only a first step. A starting conformation is also required. Once both are available simulations can be carried out using mimesis. The following are two samples from the examples in this page. On the left is a box of 500 spheres generated at random within the box. This was cooled, using molecular dynamics, to 10K (center) at which temperature the spheres condense. The effect of the finite cutoff in the van der Waals potential is evident. On the right is a realization of the circular DNA model from the batch script example. A random walk chain was generated and closed into a circle. This traps a topoisomer which appears to be very far from equilibrium.