analyzeCHARMM.pl

Usage

usage:   analyzeCHARMM.pl [options] [DCDfile(s)]
options: [-inx from:to] [-time from:to] [-step size]
         [-psf PSFfile] [-pdb PDBfile] [-crd CRDfile]
         [-comp PDBfile] [-compcrd CRDfile]
         [-timeonly]
         [-out outputfile] [-cout outputfile]
         [-log logFile] [-cmd logFile]
         [-f listfile]
         [-par CHARMMparams]
         [-custom file]
         [-custom1 file]
         [-sel Selection] [-fitsel Selection] [-selout Selection]
         [-dsel Selection Selection]
         [-tsel Selection Selection Selection]
         [-qsel Selection Selection Selection Selection]
         [-mass] [-[no]fit] [-ref x y z] [-cofm] [-ndens]
         [-rgyr] [-center] [-rms]
         [-mindist] [-maxdist] [-alldist] [-cutoff value]
         [-dist] [-angle] [-dihedral] [-pucker] [-glycosidic]
         [-phi] [-psi] [-omega] [-chi1] [-chi2] [-chi3] [-chi4] [-chi5] 
         [-epsilon] [-zeta] [-delta] [-alpha] [-beta] [-gamma]
         [-volume] [-ientropy] [-surface]
         [-rdist] [-diffusion]
         [-rmsf] [-s2] [-aniso] [-rmsdyn] [-rotcor]
         [-hbond] [-hbdist] [-hbangle] [-hbtime] [-hbunit]
         [-avg] [-orient] [-recenter] [-norotate]
         [-cpath] [-periodic] [-energy]
         [-crot]

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usage information