Hydro How-To Reference Guide

Step 1:

Since there is no graphical user interface, the program must be run from the Linux command line. The first thing to do is to make sure that the program is accessible from the computer that you are using. The easiest way to do this is to type 'hydro5alnx.exe' at the Linux command line. If you execute the command and find an error returned that looks like this:

	-bash: hydro5alnx.exe: command not found

	fmt: end of file apparent state: unit 4 named hydro.dat last
	format: (A20) lately reading sequential formatted external
	IO Aborted

Step 2:

The program will read a user-edited input file and produce an output file with the results. To avoid confusion and clutter with filenames, it is best to store these files in a separate directory. New directories can be created by using the ?mkdir directoryname? command at the Linux command line or by using an xwindows file manager. As an example we will use a directory called Hydro. Within the new base directory of Hydro, you will create subdirectories that will contain the information for the different molecules being analyzed. In this example the subdirectory will be called Moleculename. Once those directories are created, the command line in the shell window should look like this:

 
	Yourname@yourcomputer:~/Hydro/Moleculename$ 

Step 3:

You are now ready to copy the input data files to this directory. The files that you will copy in this example will be the sample files provided by the author of the software. Depending on which Hydro program in the family of programs you have chosen, the input files will vary in name and format For a description of the various programs and their purpose visit:

http://leonardo.fcu.um.es/macromol/programs/programs.htm

Although the names and format of the input files may differ for each Hydro program, all of the programs require two input files, a main input file and a structural input file. The main input file allows you to set the name of the output files, tells the program where to look for the information to manipulate(the structural input file), and sets up the experimental parameters (temperature, viscosity, ect.). A structural input data file is usually obtained experimentally and contains detailed information about the molecule to be manipulated by the program. The main input files will look like this for all versions of the program:

	TheHydroProgramName.dat example: hydropro.dat

Step 4:

From this point on, a description of how to use the HydroPro version of Hydro will be used as the model for the sample run. Note that the process is similar for all versions of the program.

Download the file called 'hydropro.dat' from the Hydropro section of the website at:

http://leonardo.fcu.um.es/macromol/programs/hydropro/hydropro.htm

When you click on the file in the table, it gives you a window with 'save as' as an option. Select this option and save the file to the 'Moleculename' subdirectory that was created earlier.

Once saved to the correct directory, view hydropro.dat using a text editor. The hydropro.dat file looks like this:

	3.1-lysozyme     !Name of molecule 
	lysozyme31       !Name for output file  
	6lyz.pdb         !Strucutural (PBD) file        
	3.1,             !AER, radius of the atomic elements 
	6,               !NSIG (number of extrapolation points
	1.0,             !Minimum radius of beads in the shell (SIGMIN)	 
	2.0,             !Maximum radius of beads in the shell (SIGMAX)	 
	293.,            !T (temperature, K) 
	0.01,            !ETA (Viscosity of the solvent in poises) 
	14320.,          !RM (Molecular weigth) 
	0.702,	         !Partial specific volume, cm3/g 
	1.0,             !Solvent density, g/cm3 
	21               !Number of values of H 
	2.e+7,           !HMAX 
	30,              !Number of intervals for the distance distribution 
	-1,              !Number of trials for MC calculation of covolume 
	1                !IDIF=1 (yes) for full diffusion tensors 
	*                !End of file 

http://leonardo.fcu.um.es/macromol/programs/hydropro/hydropro5a.pdf

The third command in the list is the most important. This tells the program where to look for the structural file, in hydropros' case this is the file with '.pdb' as its extension. This name has to be identical to the name of the structural file that you will download next. In the same table, just under the hydropro.dat file, is a file called '6lyz.pdb.' Download this file to the same subdirectory as the main file.

You are now ready to run the sample program. From the Linux command line make sure that you are in the same directory as the two files just downloaded. In this case it was '/Hydro/Moleculename.' At the command line type 'hydropro5alnx.exe' and the program will execute.

To use the program for your own experiment, simply copy the hydropro.dat file to a new directory and edit it using your own parameters. Then re-save the file using the 'save as' command under the same name in the new subdirectory. Do not change the name of hydropro.dat because the program only looks for that file name. Also, remember to change the name of the structural file to match that of your own experimental .pdb file.