MMTSB
Tool Set Documentation

Difference between revisions of "enerAmber.pl"

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It does not perform any minimization or refinement and is only useful with previously
 
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]].
 
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
 
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
 
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
 
Amber offers a number of
 
different force fields that are selected with the <font color=#508060>param</font> keyword.
 
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
 
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:
 
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>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
 
<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
 
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
 
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
 
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.
 
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
 
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
 
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>
 
which needs to be set appropriately for this script to work.<BR>

Revision as of 03:47, 31 July 2009

Usage

usage:   enerAmber.pl [options] PDBfile
options: [-out total,bonds,angles,dihedral,impropers,vdwaals,elec,gb,sasa]
         [-oneline]
         [-[no]translate]
         [-par Amberparams]
         [-log logFile]

Show source


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 enerCHARMM.pl.

Force field parameters can be given in a list of key=value pairs with -par similar to the same option in enerCHARMM.pl. 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 enerCHARMM.pl.

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