Tool Set Documentation

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usage: [options] PDBfile
options: [-par Amberparams]
         [-restart file] [-restout file]
         [-trajout file] [-final file]
         [-partop file]
         [-log file] [-elog file]
         [-l [ca|cb|cab|heavy] force refpdb min:max[=...]]
         [-cons [ca|cb|cab|heavy] refpdb min:max[_force][=...]]

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This script is used to run molecular dynamics with Amber in a similar way as with <docmark></docmark> which uses CHARMM instead. The options are very similar to <docmark></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></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.


usage information