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The Amber package is used to setup Amber input files and
run minimization jobs with Amber.
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new() |
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creates a new Amber object.
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generateTopCoor(molecule,topfile,coorfile,[parameters]) |
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generates Amber topology and coordinate files from a given Molecule object
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runSander(files) e,topfile,coorfile,outfile,logfile,restfile,
restartinfile,restartoutfile,trajinfile,trajoutfile) |
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runs Amber to perform a minimization or dynamics run. Required input are a command input file, a topology file, and a coordinate file. A restraint file is optional. The final conformation after the simulation run is completed is written to the output file given, program output is written to the log file. The methods generateTopCoor, genInputMinimize, and genInputRestraints are available to create the proper Amber files expected by this method.
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genInputDynamics(file[,parameters]) |
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generates an Amber command input file for minimization runs. A file name for the generated file is required as argument. In addition hash-type key=>value arguments may be given to set or modify minimization parameters.
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genInputMinimize(file[,parameters]) |
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generates an Amber command input file for minimization runs. A file name for the generated file is required as argument. In addition hash-type key=>value arguments may be given to set or modify minimization parameters.
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genInputRestraints(file,cons) |
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generates an Amber restraint input file from a cons data structure (see: CHARMM.pm).
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getEnergy(logfile) |
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extracts energy information from Amber output log file
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logEnergy(logfile,energylogfile) |
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produces an energy log file from the Amber output log file
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par -> { itersd, iterconj, etol, step,
gb, gbsa, cutoff, epsilon, dielec,
restrain } |
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Amber minimization parameters
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