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genpr_d
Langue: en
Version: 261658 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
genpr - generates position restraints for index groupsSYNOPSIS
genpr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -nice int -fc vector -freeze realDESCRIPTION
genpr produces an include file for a topology containing a list of atom numbers and three force constants for the X, Y and Z direction. A single isotropic force constant may be given on the command line instead of three components.WARNING: genpr only works for the first molecule. Position restraints are interactions within molecules, therefore they should be included within the correct [ moleculetype ]
block in the topology. Since the atom numbers in every moleculetype in the topology start at 1 and the numbers in the input file for genpr number consecutively from 1, genpr will only produce a useful file for the first molecule.
The -of option produces an index file that can be used for freezing atoms. In this case the input file must be a pdb file.
FILES
-f conf.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml
-n index.ndx Input, Opt.
Index file
-o posre.itp Output
Include file for topology
-of freeze.ndx Output, Opt.
Index file
OTHER OPTIONS
-[no]h noPrint help info and quit
-nice int 0
Set the nicelevel
-fc vector 1000 1000 1000
force constants (kJ mol-1 nm-2)
-freeze real 0
if the -of option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here
SEE ALSO
gromacs(7)More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre