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

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

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