enerAmber.pl - Revision history

Edit: /* Options */

2009-07-31T03:48:32Z

Options

Edit: /* Description */

2009-07-31T03:47:02Z

Description

Feig at 22:47, 7 January 2009

2009-01-07T22:47:25Z

83.3.24.91: /* Usage */

2008-11-09T21:19:48Z

Usage

69.208.255.79: /* Description */

2006-08-14T02:09:57Z

Description

69.208.255.79: /* Description */

2006-08-14T02:08:04Z

Description

Feig at 14:17, 12 August 2006

2006-08-12T14:17:13Z

New page

__NOTOC__
== Usage ==

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

== Description ==

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 <docmark>enerCHARMM.pl</docmark>.
 
Force field parameters can be given in a list of key=value pairs with -par similar
to the same option in <docmark>enerCHARMM.pl</docmark>. A list of Amber parameters
is available
<A HREF="http://mmtsb.scripps.edu/cgi-bin/amberpar" TARGET=apar>here</A>.
Amber offers a number of
different force fields that are selected with the param keyword.
Please visit the <A HREF="http://www.amber.ucsf.edu">Amber web site</A> 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 <docmark>enerCHARMM.pl</docmark>. 
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. 

== Options ==

; -help : usage information

== Examples ==

@@ Line 9: / Line 9: @@
 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><BR>
+<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
+to the same option in [[enerCHARMM.pl]]. A list of Amber parameters
 is available
-<A HREF="http://mmtsb.scripps.edu/cgi-bin/amberpar" TARGET=apar>here</A>.
+[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 <A HREF="http://www.amber.ucsf.edu">Amber web site</A> for more information on which
+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:
@@ Line 22: / Line 23: @@
 <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><BR>
+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 <docmark>enerCHARMM.pl</docmark>.<BR><BR>
+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><BR>
+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><BR>
+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>

@@ Line 8: / Line 8: @@
 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 <docmark>enerCHARMM.pl</docmark>.
+minimized structures. The script is similar in nature to the CHARMM version [[enerCHARMM.pl]].
 <BR><BR>
 Force field parameters can be given in a list of key=value pairs with <B>-par</B> similar

@@ Line 11: / Line 11: @@
 <BR><BR>
 Force field parameters can be given in a list of key=value pairs with <B>-par</B> similar
-to the same option in <docmark>enerCHARMM.pl</docmark>. A list of Amber parameters
+to the same option in [enerCHARMM.pl]. A list of Amber parameters
 is available
 <A HREF="http://mmtsb.scripps.edu/cgi-bin/amberpar" TARGET=apar>here</A>.

@@ Line 42: / Line 42: @@
 ; -help : usage information
+; -out name[,name] : specify which energy values to write out
 == Examples ==

@@ Line 1: / Line 1: @@
 __NOTOC__
-r9nURv bnnLst19hdY6llAd3fg6
+== Usage ==
 == Description ==