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Difference between revisions of "analyzeCHARMM.pl"
From MMTSB
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== Description == | == Description == | ||
+ | == 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 == | == Options == |
Revision as of 20:38, 28 February 2008
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]
Description
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