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]

Show source

Structural quantities

• Radius of gyration

 analyzeCHARMM.pl -rgyr  
 1 1 0.020000 8.39271
 2 2 0.040000 8.40157
 3 3 0.060000 8.41569
 4 4 0.080000 8.41470
 5 5 0.100000 8.40683
 ...

 analyzeCHARMM.pl -rgyr -mass        # mass weighted
 analyzeCHARMM.pl -rgyr -sel @SEL       # using C-beta atoms

• Center of geometry/mass

 analyzeCHARMM.pl -center               # center of geometry

 1 1 0.020000 0.40100 -4.63176 -2.97582
 2 2 0.040000 0.39378 -4.63659 -2.98150
 3 3 0.060000 0.40375 -4.64259 -2.97458
 4 4 0.080000 0.40161 -4.63427 -2.98087
 5 5 0.100000 0.40632 -4.63495 -2.98142

 analyzeCHARMM.pl -center -mass     # center of mass
 analyzeCHARMM.pl -center -sel @SEL    # for residues 1 to 4

• Molecular volume

 analyzeCHARMM.pl -volume               

 output contains total volume and free volume within solute cavity:
 
 1 1 0.020000 2035.228189 1.673453
 2 2 0.040000 2045.718088 2.193564
 3 3 0.060000 2073.108204 1.823200
 4 4 0.080000 2069.752854 1.300382
 5 5 0.100000 2064.565380 1.277143

• Solvent-accessible surface area

 analyzeCHARMM.pl -surface 

 1 1 0.020000 1808.42205
 2 2 0.040000 1825.50226
 3 3 0.060000 1847.81815
 4 4 0.080000 1854.86649
 5 5 0.100000 1838.83944

 analyzeCHARMM.pl -surface -par proberad=1.0           # probe radius: [0.0,100.0], def. 1.4
 analyzeCHARMM.pl -sel @SEL -surface               # select subset of structure

 analyzeCHARMM.pl -dsel @SEL1 @SEL2 -surface   # calculates surface for second set in the context of the first set

Options

-help 

usage information