solvate - surround protein with water molecules
solvate
[-tthick][-rradius][-nngauss][-ug][-ub]
[-s] [-v] [-bulk] [-w] [-ion] [-psf] [infile] outfile
SOLVATE prepares of a water shell around solutes.
solvate command.
A summary of options is included below.
- -t thick
- minimum water shell thickness in Angstrom (default: 10.0)
- -r radius
- maximum boundary curvature radius in Angstrom (default: 100000.0)
- -n ngauss
- use ngauss gaussians to define solvant boundary (default: 1)
- -s
- write surface statistics to file surface_stat.
- -v
- write volume statistics to file volume_stat.
- -ug
- use gaussians from file gaussians (skip gaussian learning phase).
- -ub
- use boundary definition from file boundary (skip gaussian learning phase
and boundary adjustment).
- -bulk
- output only bulk water (i.e., no buried water molecules)
- -w
- output only water molecules (i.e., not the solute)
- -ion
- add ions (na+/cl-) in isotonic/Debye-Hueckel concentration
- -psf
- output XPLOR-script mkpsf.inp for generating a psf-file
- infile
- pdb-file (no extension) of solute (if omitted, a water droplet is
created)
- outfile
- pdb-file (no extension) of water shell
SOLVATE was written 1996 by Helmut Grubmueller
This manual page was written by Steffen Moeller
<moeller@debian.org>, for the Debian project (but may be used by
others).