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analyzeCHARMM.pl
From MMTSB
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]
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