multipucker

Calculate specified pucker types for residues in given range.

multipucker [<name>] 
            [<pucker types>] 
            [out <filename>] 
            [resrange <range>]
            [altona|cremer] 
            [puckertype <name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] ...]
            [amplitude [ampout <ampfile>]] 
            [theta [thetaout <thetafile>]]
            [range360] [offset <offset>]  <pucker types> = nucleic furanose pyranose

[name] Output data set name.
<pucker types> Pucker types to look for (nucleic, furanose, pyranose).
[out <filename>] Output file name to write pucker data to.
[resrange ] Residue range to look for puckers in. Default is all solute residues.
[puckertype <name>:<a0>:<a1>:<a2>:<a3>:<a4>[:<a5>] Search for a custom pucker type called using atom names <a0>, <a1>, <a2>, <a3>, and <a4> (also
<a5> for 6 atom puckers).
[altona] Use method of Altona & Sundaralingam (5 atoms only). This is the default when pucker has 5 atoms.
[cremer] Use method of Cremer and Pople (5 or 6 atoms). This is the default when pucker has 6 atoms.
[amplitude] Also calculate amplitude (in degrees). ampout <ampfile> File to write amplitude sets to.
[theta] (Valid for 6 atoms only) Also calculate theta (in degrees). thetaout <thetafile> File to write theta sets to.
[range360] Wrap pucker values from 0.0 to 360.0 (default is -180.0 to 180.0).
[offset <offset>] Add <offset> to pucker values.

DataSets Generated:
<name>[<pucker type>]:<#> Aspect corresponds to the pucker type name (e.g. [nucleic], [furanose], etc). The index is the residue number.
<name>[<pucker type>Amp]:<#> amplitude only.

Data set for pucker amplitude.
<name>[<pucker type>Theta]:<#> theta only. Data set for pucker theta.

Note data sets are not generated until run is called.
Calculate specified pucker types for residues in given range. By default, puckers are identified based on standard Amber atom names. The resulting data sets will have aspect equal to [<pucker type>] and index equal to residue #. In order to be identified as a pucker, all consecutive atoms in the pucker must be bonded, and the last atom of the pucker must be bonded to the first. For example, to calculate all nucleic acid ribose puckers for residues 6 to 9:

multipucker MyPuckers nucleic resrange 6-9 out Pucker_6-9.dat

This will generate data sets named MyPuckers[nucleic]:6, MyPuckers[nucleic]:7, etc. Puckers other than those defined in <pucker types> can be searched for using pucker type. For example to create a custom pucker type called furanoid using atoms C2, C3, C4, C5, and O2, then search for and calculate that pucker (with amplitudes) using the method of Cremer and Pople in all residues:

multipucker Furanoid puckertype furanoid:C2:C3:C4:C5:O2 cremer out furanoid.dat amplitude ampout furanoid.dat

It is possible to use the statistics command to obtain the average values using:

multipucker MyPuckers nucleic resrange 1-6 out data.dat
run
statistics MyPuckers[nucleic] out data.stats