Solvate Installation on Unix and Linux Systems

To install SOLVATE, move the tar-file to your favourite directory and enter:

tar -xvzf solvate_1.0.tgz

The source solvate.c is just one ANSI-C-file without any system-specific stuff, so it should compile right away with something like

cc -ansi -O -o solvate solvate.c -lm

It is tested under IRIX System V.4 (SGI), HP-UX, and Digital UNIX V3.2C; appropriate Makefiles are included. It should now also compile without warnings on any Linux/Unix platform, thanks to Craig Jolley for posting a fix!

The distribution contains a postscript version of this manual ( as well as an html-version (html/docu.html) with references to all other files in the html-directory).

The distribution also contains two sample-solutes, bpti.pdb / bpti.psf and globh.pdb / globh.psf. To check your installation, try:

solvate -t 5.0 -n 2 -ion bpti solbpti

After several seconds you should see the following output:

  .:::::..    SOLVATE 1.0.1 (C) 1996-2010 Helmut Grubmuller

::oOOOoo:: Purpose: make a water shell around solutes



Reading solute from file bpti.pdb ... 568 atoms read.

Reading atomic charges from file bpti.psf ... total charge is +6.00 e.

Calculating bounding sphere ... done.

Creating convex volume (max. radius is 100000.000000) ... done.

Gauss-sampling convex volume ... done.

Approximating volume with 2 gaussians: Phase 1/4...2/4...3/4...4/4...done.

Saving parameter for 2 gaussians to file gaussians.lis ... done.

Adjusting boundary distance by varying gaussian widths ... 5.046 A

Gaussian widths are being scaled by a factor of 1.579210

Saving boundary parameters to file boundary.lis ... done.

Creating volume within boundary ... done.

Sorting grid points according to distance from solute ... done.

Performing distance approximation statistics with 58283 grid points ... 100%

Checking approximation for distance from boundary ... 100%

Estimated number of water molecules: 2297

Placing water molecules ... found 1692

Grouping water molecules ... 100%

The water molecules form 2 groups.

Group 1 contains 1691 water molecules

Group 2 contains 1 water molecule

So we have one single, 0 twins, and 0 triplets

Placing ions ... placed 3 sodium ions and 8 chloride ions.

Equilibrating ions (2000000 Monte Carlo moves) ... 100%

Saving solute, 1681 water molecules, and 11 ions to file solbpti.pdb ... done.

Solvate ready. No errors.

loading content