Tools and information for AMBER and CPPTRAJ examples
Updated: March 25, 2019
Undo all previous strip Action commands. Requests that the original topology and frame be used for all following actions. This has the effect of undoing any command that modifies the state (such as strip). For example, the following… Read More
Updated: March 25, 2019
Translate specified atoms by specified amounts in X/Y/Z directions. translate [<mask>] [x <dx>] [y <dy>] [z <dz>] Translate atoms in <mask> (all atoms if no mask specified) <dx> Å in the X direction, <dy> Å in the Y… Read More
Updated: September 29, 2023
Calculate system temperature using velocities of specified atoms. temperature [<name>] [out <filename>] {frame | [<mask>] [ntc <#>] [update] [remove {trans|rot|both}] … Read More
Updated: March 25, 2019
Calculate symmetry-corrected RMSD. symmrmsd [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass] [remap] [ first | reference | ref <name> | refindex <#> | previous | reftraj <name> [parm <parmname> | parmindex <#>] ] [<name>] Output data set name…. Read More
Updated: September 29, 2023
Calculate the LCPO surface area of specified atoms. Can do partial surface areas. surf [<name>] [<mask1>] [out <filename>] [solutemask <mask>] [offset <offset>] [nbrcut <cut>] <name> Output data set name. <mask1> Atoms to calculate surface area for. out <filename>… Read More
Updated: March 25, 2019
Alternative translational diffusion calculation which can calculate diffusion in specified regions. stfcdiffusion mask <mask> [out <file>] [time <time per frame>] [mask2 <mask>] [lower <distance>] [upper <distance>] [nwout <file>]) [avout <file>] [distances] [com] [x|y|z|xy|xz|yz|xyz] mask <mask> Atoms for which… Read More
Updated: March 25, 2019
SPAM method for estimating relative free energies of waters in hydration shell around proteins. spam <filename> [solv <solvname>] [reorder] [name <name>] [purewater] [cut <cut>] [info <infofile>] [summary <summary>] [site_size <size>] [sphere] [out <datafile>] [dgbulk <dgbulk>] [dhbulk <dhbulk>] [temperature… Read More
Updated: March 25, 2019
Set velocities for specified atoms using Maxwellian distribution based on given temperature. setvelocity [<mask>] [tempi <temperature>] [ig <random seed>] [<mask>] Mask of atoms to assign velocities to. [tempi <temperature>] Assign velocities at specified temperature (default 300.0 K). [ig… Read More
Updated: March 25, 2019
Scale coordinates in X/Y/Z directions by specified factors. scale x <sx> y <sy> z <sz> <mask> Scale the X|Y|Z coordinates of atoms in <mask> by <sx>|<sy>|<sz>.
Updated: March 25, 2019
Calculate the running average of coordinates over specified window size. runavg [window <window_size>] Note that for backwards compatibility with ptraj runningaverage is also accepted. Replaces the current frame with a running average over a number of frames specified… Read More
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