analyzeCHARMM.pl

usage: analyzeCHARMM.pl [options] [DCDfile(s)] options: [-inx from:to] [-time from:to] [-step size]

        [-psf PSFfile] [-pdb PDBfile] [-crd CRDfile] [-comp PDBfile]
        [-timeonly]
        [-out outputfile]
        [-log logFile] [-cmd logFile]
        [-f listfile]
        [-par CHARMMparams]
        [-custom file]
        [-sel Selection] [-fitsel 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]
        [-dist] [-angle] [-dihedral] [-pucker] [-glycosidic]
        [-phi] [-psi] [-omega] [-chi1]
        [-epsilon] [-zeta] [-delta] [-alpha] [-beta] [-gamma]
        [-volume] [-ientropy] [-surface]
        [-rdist] [-diffusion]
        [-rmsf] [-s2]
        [-avg] [-orient]

Options

-help 

usage information

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

Geometric quantities

• Distances

 analyzeCHARMM.pl -dist -dsel @SEL1 @SEL2

 calculates distance between individual atoms or center of geometry/mass if selection includes
 more than one atom

 1 1 12241.200000 14.11953
 2 2 12241.400000 14.27596
 3 3 12241.600000 14.09303
 4 4 12241.800000 14.60734
 5 5 12242.000000 14.50452

 analyzeCHARMM.pl -dist -dsel @SEL1 @SEL2 -mass   # use center of mass instead of geometry

• Minimum distance

 analyzeCHARMM.pl -mindist -dsel @SEL1 @SEL2

 calculates the minimum distance between two sets of atoms and lists which atoms form the
 closest pair

 1 1 12241.200000 9.8103 PRO0:MET:1:HG1 PRO0:LEU:5:N
 2 2 12241.400000 10.2972 PRO0:MET:1:O PRO0:LEU:5:N
 3 3 12241.600000 10.0149 PRO0:MET:1:HG1 PRO0:LEU:5:N
 4 4 12241.800000 10.0283 PRO0:MET:1:O PRO0:LEU:5:N
 5 5 12242.000000 10.3612 PRO0:MET:1:HG1 PRO0:LEU:5:N

• Maximum distance

 analyzeCHARMM.pl -maxdist -dsel @SEL1 @SEL2

 calculates the maximum distance between two sets of atoms and lists which atoms form the
 farthest pair

 1 1 12241.200000 18.5360 PRO0:MET:1:HE1 PRO0:LEU:5:HD22
 2 2 12241.400000 18.2772 PRO0:MET:1:HE2 PRO0:LEU:5:HD22
 3 3 12241.600000 18.2094 PRO0:MET:1:HE1 PRO0:LEU:5:HD22
 4 4 12241.800000 18.7409 PRO0:MET:1:HE1 PRO0:LEU:5:HD22
 5 5 12242.000000 18.5781 PRO0:MET:1:HE1 PRO0:LEU:5:HD22

• Angle

 analyzeCHARMM.pl -angle -tsel @SEL1 @SEL2 @SEL3 [-mass]

 calculates the angle spanned by three atoms or centers of geometry/mass

 1 1 12241.200000 144.775
 2 2 12241.400000 143.582
 3 3 12241.600000 149.128
 4 4 12241.800000 146.636
 5 5 12242.000000 145.757

• Dihedral

 analyzeCHARMM.pl -dihedral -qsel @SEL1 @SEL2 @SEL3 @SEL4 [-mass]

 calculates the dihedral spanned by four atoms or centers of geometry/mass

 1 1 12241.200000 177.110
 2 2 12241.400000 176.090
 3 3 12241.600000 173.423
 4 4 12241.800000 171.144
 5 5 12242.000000 170.831

• Peptide torsions

 analyzeCHARMM.pl -phi|-psi|-omega|-chi1 -sel @SEL

 calculates standard peptide torsions phi/psi/omega/chi1 for the residues selected
 in the given selection.

 1 1 12241.200000 -107.801 -115.927
 2 2 12241.400000 -123.998 -129.870
 3 3 12241.600000 -114.029 -132.415
 4 4 12241.800000 -118.533 -119.548
 5 5 12242.000000 -128.236 -116.957

• Nucleic acid backbone torsions

 analyzeCHARMM.pl -epsilon|-zeta|-delta|-alpha|-beta|-gamma -sel @SEL

 calculates standard nucleic acid backbone torsions for the residues selected
 in the given selection.

 1 1 12241.200000 -107.801 -115.927
 2 2 12241.400000 -123.998 -129.870
 3 3 12241.600000 -114.029 -132.415
 4 4 12241.800000 -118.533 -119.548
 5 5 12242.000000 -128.236 -116.957

• Nucleic acid sugar pucker

 analyzeCHARMM.pl -pucker -sel @SEL

 calculates the sugar pucker phase and amplitude for the residues selected in
 the given selection

 1 1 3.825000 134.90 50.3298
 2 2 3.900000 123.16 48.9725
 3 3 3.975000 131.20 50.0423
 4 4 4.050000 143.38 41.2196
 5 5 4.125000 169.54 41.9678

• Nucleic acid glycosidic torsion

 analyzeCHARMM.pl -glycosidic -sel @SEL

 calculates the glycosidic torsion for the residues selected in
 the given selection

 1 1 3.825000 -169.625
 2 2 3.900000 -176.319
 3 3 3.975000 -172.100
 4 4 4.050000 -160.011
 5 5 4.125000 -158.718

Comparison with reference

• Coordinate root mean square displacement

 analyzeCHARMM.pl -rms -sel @SEL -comp @REFPDB

 calculates the RMSD with respect to reference PDB after least-squares superposition

 1 1 3.825000 2.733075
 2 2 3.900000 2.724830
 3 3 3.975000 2.736593
 4 4 4.050000 2.726076
 5 5 4.125000 2.720903

 analyzeCHARMM.pl -nofit -rms -sel @SEL -comp @REFPDB         # do not fit structure
 analyzeCHARMM.pl -rms -sel @SEL1 -fitsel @SEL2 -comp @REFPDB  # superimpose different part of the structure than the part for which RMSD is calculated

Distribution functions

• Radial distribution function

 analyzeCHARMM.pl -rdist -dsel @SEL1 @SEL2  

 calculates the normalized radial distribution function of atoms in set 1 
 with respect to atoms in set 2 

 0.157960 0.000000
 0.315930 0.000000
 0.473890 0.000000
 0.631860 0.000000
 0.789820 0.000000
 0.947780 0.000000
 1.105700 0.000000
 1.263700 0.000000
 1.421700 0.000000
 1.579600 0.000373
 1.737600 0.011711
 1.895600 0.054040
 2.053500 0.065664
 2.211500 0.056921
 2.369500 0.088735
 2.527400 0.214377
 2.685400 0.418000

 analyzeCHARMM.pl -rdist -dsel @SEL1 @SEL2 -ndens        # report number density
 analyzeCHARMM.pl -rdist -dsel @SEL1 @SEL2 -cofm         # use center of mass of second selection
 analyzeCHARMM.pl -rdist -sel @SEL1 -ref x y z           # use fixed reference point
 analyzeCHARMM.pl -rdist -par rdfbins=100                # set number of bins
 analyzeCHARMM.pl -rdist -par rdfrmax=10.0               # set maximum value

Dynamic parameters

• Root mean square fluctuation

 analyzeCHARMM.pl -rmsf -sel @SEL   

 calculates the root mean square fluctuation for the selected atoms

 PRO0:ALA:1:CAY 16.379000
 PRO0:ALA:1:CY 16.146000
 PRO0:ALA:1:OY 16.115000
 PRO0:ALA:1:N 16.134000
 PRO0:ALA:1:CA 16.102000
 PRO0:ALA:1:CB 16.327000
 PRO0:ALA:1:C 16.065000
 PRO0:ALA:1:O 16.290000
 PRO0:ALA:1:NT 15.935000
 PRO0:ALA:1:CAT 16.062000

Common parameters

• @ATOP

 topology information for analyzeCHARMM.pl:
 -pdb file.pdb
 -par blocked -pdb file.pdb
 -par param=simdb -pdb file.pdb  
 -psf file.psf

• @DCD

 DCD file name

• @SEL

 atom/residue selection string