View source for enerAmber.pl

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== Usage ==

<mmtsbToolUsage cmd="enerAmber.pl"></mmtsbToolUsage>

== Description ==

This script uses Amber to evaluate the energy of a protein structure from a PDB file.<BR>
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 [[enerCHARMM.pl]].
<BR>

Force field parameters can be given in a list of key=value pairs with <B>-par</B> similar
to the same option in [[enerCHARMM.pl]]. A list of Amber parameters
is available
[http://feig.bch.msu.edu/mmtsb/Amber_Parameters here].
Amber offers a number of
different force fields that are selected with the <font color=#508060>param</font> keyword.
Please visit the [http://ambermd.org 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 <font color=#508060>gb</font>. The tags correspond to the author names as follows:
<font color=#508060>tc</font>: Tsui & Case, <font color=#508060>tc6</font> Tsui & Case (original radii),
<font color=#508060>obc</font>: Onufriev, Bashford, Case, <font color=#508060>jsb</font>: Jayaram, Sprous, Beveridge,
<font color=#508060>mgb</font>: modified Jayaram, Sprous, Beveridge. Again, more information is available
on the Amber web site.<BR>

Once the energies have been evaluated the total energy or some or all components may be
written to standard output. The flag <B>-out</B> is used to specify a list of desired
energy values as in [[enerCHARMM.pl]].<BR>

The option <B>-translate</B> or <B>-notranslate</B> 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 (<B>-translate</B>).<BR>

The option <B>-log</B> is available to save the complete
output from Amber under the given file name.<BR>

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.<BR>

== Options ==

; -help : usage information
; -out name[,name] : specify which energy values to write out
; -oneline : output data in a single line
; -[no]translate : (do not) translate input PDB
; -par key=value[,...] : Amber simulation parameters
; -log file : Amber log file

== Examples ==