PELE

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Protein Energy Landscape Explorer (PELE) Victor Guallar Lab

Possible Paramters

      res [2 word PLOP res list]   : Define a ligand using either the first and last residue or any other 
                                   : Standard PLOP method of defining a group of resideus ie A:1 A:10.
                                   : Multiple ligands can be defined and parameters specfic to the ligand should be 
                                   : set directly following the residue selection.  See ligand parameters section of the manual
                                   : for more details.
      het [residue name]           : Define a ligand as a single residue using standard PLOP residue format ie _:1
                                   : Multiple ligands can be defined and parameters specfic to the ligand should be 
                                   : set directly following the residue selection.  See ligand parameters section of the manual
                                   : for more details.
      debug [yes/NO]               : Turn on or off debuging output including printing of frames at different stages
                                   : Within a step
      verbose [yes/NO]             : Turn on extra output
      save_type [integer]          : Choose one of several methods for saving frames for potential spawning at a later time
                                   : 1 - Default - Store the frame with the best value (determined by spawning) for each 
                                   :     metric that is being used for spawning
                                   : 3 - Maximal - Store All the frames.  Only discards those frames that would immediately 
                                   :     Spawn to another stored frame.
                                   : 4 - Recent - Save the Current Configuration on each processor.
      save_median_freq [integer]   : Caculate the median of the stored configurations (the median structure if using save_type 4)
                                   : every this number of steps on ALL processors.  This is used for several metrics refering
                                   : to the median structure. The default is 5 times the number of processors.
      init_min(imization) [YES/no] : Whether to start with a full minimization of the system.
      show_stor(ed) [yes/NO]       : Whether to show a list of the stored geometries in the output.
      drive_type [integer]         : 0 - default - Do not perform backbone moves
                                   : 1 - When perturbing based on rotamer libaries in the backbone use the rotamer libraries to 
                                   :               determine the rotatable angles, but choose randomly
                                   : 2 - use libs - Use rotamer angles for angles and values
      rem_bulk_mov(e)              : 3 - Superpose the backbone CA with the previous position after every step
                                   : 1 - (default) Only after relaxation steps (not currently implemented)
      steric_tr(ies) [integer]     : Maximum number of tries to find a confirnmation that doesn't produce steric clash
                                   : including the possibility for rearrangements in side chains (100)
      tries [integer]              : Generate this number of potenital (non-clashing) potential pertubations and choose
                                   : the one with the lowest energy in the homology modelign potential (default 1)
      lcom_constraint [real]       : Add a constraint to keep the ligand com (or com atom ) from moving too much after driving
                                   : default 0.0 
      mifre [integer]              : Run the minimization every this number of cycles (default 1 = every cycle)
      spfre [integer]              : Run the side chain prediction every this number of cycles (default 1 = every cycle)
      anmfre [integer]             : Run the anm move every this number of cycles (default 1 = every cycle)
      ldfre [integer]              : Generate a ligand pertubation every this number of cycles (default 1 = every cycle)
      wrfre [integer]              : Write an output frame every this number of cycles (default 5 = every 5th cycle)
      path [filename]              : Write output frames based on this name
      pdbmodel <YES/no>            : Write output as pdb files with multiple models 
      st_wrfre [integer]           : Write an output frame every this number of times a frame is stored (default -1 = never)
      minrmsd [ distance (a) ]     : If steering, keeps the same direction if the RMSD change generated was more than this 
                                   : (default 0.0) 
      waitfor [ integer ]          : If steering, keep the same direction for this number of steps.
      rot_r(ange) [angle radians]  : In the pertubation, rotate the ligand by a random amount +/-50% from this value (def 0)
      tra_r(ange) [dist A]         : In the pertubation, translate the ligand by a random amount +/-50% from this value (def 0)
      tight [real]                 : The tightness around the steering vector for steering
      temp(erature) [Kelvin]       : Metropolis temprature      
      sprad [distance A]           : Range around the ligand to run a sidechain prediction
      anmrad [distance A]          : Range around the ligand to run a sidechain prediction
      mirad [distance A]           : Range around the ligand to run a minimization
      omit_sp [2 word res list]    : Always omit these residues from sidechain predictions (example format A:10 A:12)
      omit_anm [2 word res list]   : Always omit these residues from anm
      omit_mi [2 word res list]    : Always omit these residues from minimizations (example format _:1 _:5A )
      omit_res [2 word res list]   : Always omit these residues from sidehcian prediction and minimizations 
      omit [filename]              : Depreciated way to omit residues (use "omit_res file my_filename" instead)
      sideadd [2 word res list]    : Always add the following residues to the sidechain prediction
      anmadd [2 word res list]     : Always add the following residues to the sidechain prediction
      minadd [2 word res list]     : Always add the following residue to the minimization
      min_atom file [filename]     : Always add the following atoms to the minimization file format is one per line using
                                   : standard PLOP atom format (ie A:10:_CA_)
      min_atom [atom name]         : Always add the following atom to the miniztion (format ex _:10:_CB_)
      side [...] sideend           : Send the following parameters to the sidechain prediction routine  
      min [...] minend             : Send the following parameters to the minimization routine (not including the ANM minimization)
      dyn [...] dynend             : Send the following parameters to the molecular dynamics routine (optional) 


PELE Metrics (used for tasks)


PELE Tasks (exiting tasks, Spawning and conditional paramters)

Showing Metrics

    show [metric]
    Simply prints out a metric in the table after each step.  These can be easily compiled/plotted with PlotMetric.pl
    All metrics involved in spawning, exiting etc are automatically printed as well.

Combining Metrics and other Advanced uses Up to 5 metrics can be combined for any of the above tasks (if,spawn,exit but not show). They are combined with a logical "and". In cases where multiple stored geometries fufill the requiredments for spawning the first metric in the combination take precedence (ie. spawn energy lt 5 rmsd_sys heavy within 1.0 would spawn to the lowest energy geometry if there were multiple stored geometries with an energy 5kcals/mole lower and differing by less than 1.0 RMSD from the native structure.)

It is also possible to have negative values if the conditionals. "energy lt -5" should be read as the energy should not increase by more then 5kcals/mole in any spawn. Such a conditional should usually be combined with another. In the previous example " spawn energy lt -10 rmsd_sys heavy within 1.0 " would keep the system within 1.0A RMS of the native while not allowing large energy increases to due so. As a side effect it will also spawn to the lowest energy structure within 1.0A RMSD of the native ( as the energy metric is listed first in the conditional ) so it will sample until the RMSD to the native is more than 1A and then restart from the lowest energy structure in the 1A RMSD region.

PELE ANM bindings (used for ANM moves)

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