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       g_dyndom - interpolate and extrapolate structure rotations

       VERSION 4.0.1


       g_dyndom  -f  dyndom.pdb -o rotated.xtc -n domains.ndx -[no]h -nice int
       -firstangle real -lastangle real -nframe int -maxangle real -trans real
       -head vector -tail vector


       g_dyndom     reads     a     pdb     file     output     from    DynDom It  reads  the  coordinates,  and  the
       coordinates  of  the  rotation  axis furthermore it reads 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  g_confrms) 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


       -f dyndom.pdb Input
        Protein data bank file

       -o rotated.xtc Output
        Trajectory: xtc trr trj gro g96 pdb

       -n domains.ndx Input
        Index file


        Print help info and quit

       -nice int 0
        Set the nicelevel

       -firstangle real 0
        Angle of rotation about rotation vector

       -lastangle real 0
        Angle of rotation about rotation vector

       -nframe int 11
        Number of steps on the pathway

       -maxangle real 0
        DymDom dtermined angle of rotation about rotation vector

       -trans real 0
        Translation (Aangstroem) along rotation vector (see DynDom info file)

       -head vector 0 0 0
        First atom of the arrow vector

       -tail vector 0 0 0
        Last atom of the arrow vector



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                    g_dyndom(1)