mdAmber.pl - Revision history

Edit: /* Options */

2009-07-31T03:55:35Z

Options

Edit: /* Options */

2009-07-31T03:55:07Z

Options

Edit: /* Description */

2009-07-31T03:50:24Z

Description

192.26.250.230: /* Description */

2006-08-12T17:55:00Z

Description

Feig at 14:18, 12 August 2006

2006-08-12T14:18:10Z

New page

__NOTOC__
== Usage ==

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

== Description ==

This script is used to run molecular dynamics with Amber in a similar
way as with <docmark>mdCHARMM.pl</docmark> which uses CHARMM instead.
The options are very similar to <docmark>minAmber.pl</docmark>.
At this point the focus is on running implicit solvent dynamics.
Explicit water simulations are not supported yet but this
feature will be added in the near future. 

Output file names can be set with the following options: -final
is used for the final conformation in PDB format, -trajout is used
to request a coordinate trajectory file, and a restart file is written
out with -restout. In a subsequent simulation, a restart file
is read in at the beginning if given with -restart. No Amber parameter
file needs to be generated prior to using this utility, but if an appropriate
parameter/topology file is available it may be given with -partop. 

As in <docmark>minAmber.pl</docmarl> the location of the Amber binary and
data directory are expected
from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least
AMBERHOME should be set accordingly. Otherwise an
attempt is made to locate the Amber binary from the search path and deduce the data
directory from the binary location. The current version of this utility expects
Amber 7 or newer for full functionality. 

== Options ==

; -help : usage information

== Examples ==

@@ Line 42: / Line 42: @@
 ; -l [ca|cb|cab|heavy] force refpdb min&#58;max[=...] : restrain sampling outside specified residue range
 ; -cons [ca|cb|cab|heavy] refpdb min&#58;max[_force][=...] : restrain sampling for specified residue range
 == Examples ==

@@ Line 11: / Line 11: @@
 At this point the focus is on running implicit solvent dynamics.
 Explicit water simulations are not supported yet but this
-feature will be added in the near future.<BR><BR>
+feature will be added in the near future.<BR>
 Output file names can be set with the following options: <B>-final</B>
@@ Line 19: / Line 19: @@
 is read in at the beginning if given with <B>-restart</B>. No Amber parameter
 file needs to be generated prior to using this utility, but if an appropriate
-parameter/topology file is available it may be given with <B>-partop</B>.<BR><BR>
+parameter/topology file is available it may be given with <B>-partop</B>.<BR>
 As in [[minAmber.pl]] the location of the Amber binary and
@@ Line 27: / Line 27: @@
 attempt is made to locate the Amber binary from the search path and deduce the data
 directory from the binary location. The current version of this utility expects
-Amber 7 or newer for full functionality.<BR><BR>
+Amber 7 or newer for full functionality.<BR>
 == Options ==

@@ Line 32: / Line 32: @@
 ; -help : usage information
+; -par key=value[,...] : Amber simulation parameters
 == Examples ==

@@ Line 7: / Line 7: @@
 This script is used to run molecular dynamics with Amber in a similar
-way as with <docmark>mdCHARMM.pl</docmark> which uses CHARMM instead.
+way as with [[mdCHARMM.pl]] which uses CHARMM instead.
-The options are very similar to <docmark>minAmber.pl</docmark>.
+The options are very similar to [[minAmber.pl]].
 At this point the focus is on running implicit solvent dynamics.
 Explicit water simulations are not supported yet but this
@@ Line 21: / Line 21: @@
 parameter/topology file is available it may be given with <B>-partop</B>.<BR><BR>
-As in <docmark>minAmber.pl</docmarl> the location of the Amber binary and
+As in [[minAmber.pl]] the location of the Amber binary and
 data directory are expected
 from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least
@@ Line 28: / Line 28: @@
 directory from the binary location. The current version of this utility expects
 Amber 7 or newer for full functionality.<BR><BR>
 == Options ==