Man page - solvate(1)

Manual

solvate - surround protein with water molecules

solvate [-t thick] [-r radius] [-n ngauss] [-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).