MMTSB
Tool Set Documentation

analyzeCHARMM.pl

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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


Options

-help 
usage information
-inx from
to : analyze the specified frame range from trajectory file
-time from
to : analyze the specified time range from trajectory file
-step size 
skip the specified number of steps in between frame analyses
-psf PSFfile 
use the specified protein structure file (PSF)
-pdb PDBfile 
use the specified PDB file
-crd CRDfile 
use the specified coordinate file (CRD)
-comp PDBfile 
load a reference PDB file into the comparison coordinate set
-timeonly 
write out only time
-out outputfile 
generate a new trajectory file (see -orient)
-log logFile 
generate CHARMM log file
-cmd logFile 
generate CHARMM input file
-f listfile 
analyze the trajectory files given in the list
-par CHARMMparams 
use specified CHARMM parameters (see CHARMM_Parameters)
-custom file 
custom CHARMM commands to be read at every analysis step
-custom1 file 
custom file that is only read once
-sel Selection 
analyze given selection
-fitsel Selection 
fit with respect to the comparison set based on the given selection
-dsel Selection Selection 
double selection used for distance measurements, etc
-tsel Selection Selection Selection 
triple selection used for angle measurements, etc
-qsel Selection Selection Selection Selection 
quadruple selection used for dihedral angle measurements, etc
-mass 
use mass weighted fitting
-[no]fit 
perform least-squares superposition before analyzing (see -fitsel)
-ref x y z 
use fixed reference point
-cofm 
use center-of-mass for selection
-ndens 
report number density
-rgyr 
calculate the radius of gyration
-center 
calculate the center of geometry
-rms 
calculate the root mean square deviation
-mindist 
calculate the minimum distance
-maxdist 
calculate the maximum distance
-dist 
calculate the distance between two selections
-angle 
calculate the angle between three selections
-dihedral 
calculate the dihedral angle between four selections
-pucker 
calculate the sugar pucker for a given nucleotide
-glycosidic 
calculate the glycosidic bond type for a given nucleotide
-phi 
calculate the phi backbone dihedral angle for a given selection
-psi 
calculate the psi backbone dihedral angle for a given selection
-omega 
calculate the omega backbone dihedral angle for a given selection
-chi1 
calculate the chi1 sidechain dihedral angle for a given selection
-chi2 
calculate the chi2 sidechain dihedral angle for a given selection
-chi3 
calculate the chi3 sidechain dihedral angle for a given selection
-chi4 
calculate the chi4 sidechain dihedral angle for a given selection
-chi5 
calculate the chi5 sidechain dihedral angle for a given selection
-epsilon 
calculate the epsilon backbone dihedral angle for a given selection
-zeta 
calculate the zeta backbone dihedral angle for a given selection
-delta 
calculate the delta backbone dihedral angle for a given selection
-alpha 
calculate the alpha backbone dihedral angle for a given selection
-beta 
calculate the beta backbone dihedral angle for a given selection
-gamma 
calculate the gamma backbone dihedral angle for a given selection
-volume 
calculate the molecular volume
-ientropy 
calculate entropy from moment of inertia
-surface 
calculate the solvent accessible surface area
-rdist 
calculate the normalized radial distribution function of atoms in one selection with respect to atoms in another selection
-diffusion 
calculate diffusion constant
-rmsf 
calculate the root mean square fluctuation
-s2 
calculate NMR order parameters
-avg 
calculate average conformation
-orient 
orient each trajectory frame

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

Clustering/Average

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


Energetics

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