gorex.pl

Usage

usage:   convpdb.pl [options] [PDBfile]
options: [-center] [-translate dx dy dz] [-orient]
         [-rotate m11 m12 m13 m21 m22 m23 m31 m32 m33]
         [-rotatex phi] [-rotatey phi] [-rotatez phi]
         [-biomt num] [-smtry num]
         [-scale factor] [-diff PDBfile] [-difflsqfit] [-add PDBFile]
         [-nmode file amplitude weight]
         [-nmodesample file prefix from to delta] [-skipzero]
         [-sel list] [-exclude list]
         [-chain id] [-model num] [-firstmodel] [-nohetero]
         [-selseq abbrev]
         [-nsel Selection]
         [-merge pdbfile]
         [-renumber start] [-addres value]
         [-renumwatersegs]
         [-match pdbfile]
         [-setchain id] [-setseg id] [-setall]
         [-readseg] [-chainfromseg] [-splitseg] [-alternate]
         [-charmm19] [-amber]
         [-out charmm19 | charmm22 | amber | generic]
         [-genres]
         [-crd] [-crdext] [-crdinp]
         [-segnames]
         [-fixcoo]
         [-ssbond res1:res2[=res1:res2]] [-nossbond]
         [-solvate] [-cutoff value] [-solvcut value]
         [-octahedron] [-cubic]
         [-ions NAME:num[=NAME:num]]
         [-replace PDB:num]
         [-info] [-listseg] [-residues] [-rescount]
         [-fill inx:seq]
         [-mol2]
         [-cleanaux]
         [-setaux1 value] [-setaux2 value]
         [-removeclashes] [-clashes] [-clashcut value]
         [-wrap boxx boxy boxz] [-by chain|atom|system]
         [-reimage cx cy cz]

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Description

This script is used to run replica exchange simulations for Ca-only Go-models based on the Karanicolas and Brooks <a href="http://www.mmtsb.org/webservices/gomodel.html">Go-model Builder</a>. In most parallel environments it will start the replica exchange server automatically. The options -n, -par, -temp, -condfile, -ens, -ensdir are available as in <docmark>rexserver.pl</docmark>. Alternatively, it can connect to an external replica exchange server if its address, port, and ID are given with -rserv. In that case -jobs may be used to run only some of the temperature windows instead of all windows if multiple clients are launched on different machines.

For shared memory environments the option -cpus can be used to specify a smaller number of CPUs than temperature windows if necessary due to computational restraints. A host file can be given with -hosts for automatic remote submission in a distributed environment. (see <docmark>calcprop.pl</docmark> for a more detailed explanation).

In order to contact the server from an external program (e.g. for monitoring purposes) the server ID is required. The option -saveid is available to write this server information to a file.

The intial input PDB and parameter/toplology files for each MD simulation are given by the last command line argument in the form PREFIX, where this is the identifier following the GO_PREFIX in the files returned by the Go Builder. Additionally, different PDB coordinate files can be can be used to start each simulation. They are read from an external file that is given with -f. The remaining parameters are used to control the MD simulations. Parameters that can be given with -mdpar are shown <A HREF="http://www.mmtsb.org/cgi-bin/charmmpar" TARGET=cpar>here</A>. Further options given with -mdopt control whether a trajectory or energy file is written out ([no]trajout and [no]enerout).

The simulation protocol can be further customized by providing CHARMM commands through external files. This can be done with -custom which expects a keyword and a file name as arguments. The keyword is used to specify when the custom command sequence should be inserted in the standard protocol. If setup is used the commands will be sent to CHARMM only once during the initial setup phase. If the keywords pre or post the commands will be executed before or after the dynamics command, respectively. These keywords can be further qualified with :init, :equi, and :prod corresponding to the replica exchange cycle modes to allow custom equilibration protocols.

The option -log is available to request a server log file. A CHARMM log file is generated for each client if -charmmlog is given, an energy log file is generated with -elog.