Tool Set Documentation

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usage: [options] PDBfile
options: [-out total,bonds,angles,dihedral,impropers,vdwaals,elec,gb,sasa]
         [-par Amberparams]
         [-log logFile]

Show source


This script uses Amber to evaluate the energy of a protein structure from a PDB file.
It does not perform any minimization or refinement and is only useful with previously minimized structures. The script is similar in nature to the CHARMM version

Force field parameters can be given in a list of key=value pairs with -par similar to the same option in A list of Amber parameters is available here. Amber offers a number of different force fields that are selected with the param keyword. Please visit the Amber web site for more information on which force field may be most appropriate. Amber implements a number of different Generalized Born models that are selected with gb. The tags correspond to the author names as follows: tc: Tsui & Case, tc6 Tsui & Case (original radii), obc: Onufriev, Bashford, Case, jsb: Jayaram, Sprous, Beveridge, mgb: modified Jayaram, Sprous, Beveridge. Again, more information is available on the Amber web site.

Once the energies have been evaluated the total energy or some or all components may be written to standard output. The flag -out is used to specify a list of desired energy values as in

The option -translate or -notranslate is available to specify whether the input PDB file is already in Amber format or whether atom and residue name conversions are necessary. By default, it is assumed that the input file is not in Amber format (-translate).

The option -log is available to save the complete output from Amber under the given file name.

The location of the Amber binary and data files are set from the environment variables AMBERHOME which needs to be set appropriately for this script to work.


usage information
-out name[,name] 
specify which energy values to write out
output data in a single line
(do not) translate input PDB
-par key=value[,...] 
Amber simulation parameters
-log file 
Amber log file