.TH g_dyndom 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_dyndom - interpolate and extrapolate structure rotations

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "\-f" " dyndom.pdb "
.BI "\-o" " rotated.xtc "
.BI "\-n" " domains.ndx "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-firstangle" " real "
.BI "\-lastangle" " real "
.BI "\-nframe" " int "
.BI "\-maxangle" " real "
.BI "\-trans" " real "
.BI "\-head" " vector "
.BI "\-tail" " vector "
.SH DESCRIPTION
\&\fB g_dyndom\fR reads a \fB .pdb\fR file output from DynDom
\&(http://www.cmp.uea.ac.uk/dyndom/).
\&It reads the coordinates, the coordinates of the rotation axis,
\&and an index file containing the domains.
\&Furthermore, it takes the first and last atom of the arrow file
\&as command line arguments (head and tail) and
\&finally it takes the translation vector (given in DynDom info file)
\&and the angle of rotation (also as command line arguments). If the angle
\&determined by DynDom is given, one should be able to recover the
\&second structure used for generating the DynDom output.
\&Because of limited numerical accuracy this should be verified by
\&computing an all\-atom RMSD (using \fB g_confrms\fR) rather than by file
\&comparison (using diff).


\&The purpose of this program is to interpolate and extrapolate the
\&rotation as found by DynDom. As a result unphysical structures with
\&long or short bonds, or overlapping atoms may be produced. Visual
\&inspection, and energy minimization may be necessary to
\&validate the structure.
.SH FILES
.BI "\-f" " dyndom.pdb" 
.B Input
 Protein data bank file 

.BI "\-o" " rotated.xtc" 
.B Output
 Trajectory: xtc trr trj gro g96 pdb 

.BI "\-n" " domains.ndx" 
.B Input
 Index file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-firstangle"  " real" " 0     " 
 Angle of rotation about rotation vector

.BI "\-lastangle"  " real" " 0     " 
 Angle of rotation about rotation vector

.BI "\-nframe"  " int" " 11" 
 Number of steps on the pathway

.BI "\-maxangle"  " real" " 0     " 
 DymDom dtermined angle of rotation about rotation vector

.BI "\-trans"  " real" " 0     " 
 Translation (Angstrom) along rotation vector (see DynDom info file)

.BI "\-head"  " vector" " 0 0 0" 
 First atom of the arrow vector

.BI "\-tail"  " vector" " 0 0 0" 
 Last atom of the arrow vector

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.