NAME

       solvate - surround protein with water molecules

SYNOPSIS

       solvate [-tthick][-rradius][-nngauss][-ug][-ub]
                      [-s] [-v] [-bulk] [-w] [-ion] [-psf] [infile] outfile

DESCRIPTION

       SOLVATE prepares of a water shell around solutes.

       solvate command.

OPTIONS

       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

SEE ALSO

AUTHOR

       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).

                                        Dezember 28, 2007                              SOLVATE(1)