NAME

mkchainarc - generate a biased random walk chain

SYNOPSIS

mkchainarc -n N_atom -at textarch [ options ]

DESCRIPTION

A biased random walk chain is generated for N_atom atoms for a reduced representation model of RNA and write to a text format archive file textarch. (The file has to be converted to binary form before it can be used in simulations - see arc.) In this reduced representation model, each nucleotide is represented by a single pseudo-atom (P) which is positioned roughly at the phosphate.

The options are:

-bond0 b_o: specify the distance between the P atoms; the preset value is 6.1Å.

-thetamax q_o: specify the maximum angle spanned by three successive P atoms, P-P-P; the preset value is 30 degrees. Each angle will be selected as a random quantity from 0 to q_o degrees.

The random chain is generated with successive P atoms placed b_oÅ apart, with every third P atom at a random angle varying from 0 to q_o degrees from the previous two atoms and with every third and fourth P atoms at a torsion angle from the earlier two atoms at a random angle from 0 to 180 degrees. There is no user control over the maximum torsion angle.

EXAMPLES

mkchainarc -n 120 -thetamax 20 -at 5SRNA.at

Generate a random chain 120 P-atoms long with the angles varying from 0 to 20 degrees and write the output as a text archive to the file 5SRNA.at.

FILES

SEE ALSO

arc, mkr2cc, mksnac, mkchaindes

DIAGNOSTICS

If the file specified after the -at option already exists, you will be warned and no chain will be generated. The existing file will not be touched. A new file name must be specified for the program to complete.

BUGS

NOTES

mkchainarc is part of the suite of utilities for the modeling of reduced representation RNA. The RNA is represented at differing levels, varying from very low resolution where helical regions are represented by a few atoms to a low resolution level where each nucleotide is represented by a single pseudo-atom. The other utilities in tis suite are: mksnad, mksnac, xmr2 and mkchaindes.