Installation of Amber 6

To compile the basic AMBER distribution, do the following:

1. Set up the $AMBEHROME environment variable to point to where the Amber tree resides on your machine. For example

   Using csh, tcsh, etc: setenv AMBERHOME /thr/gamow/amber6
   

   
   Using sh, zsh, etc: set AMBERHOME=/thr/gamow/amber6
   export AMBERHOME
   

   
   NOTE: Be sure to replace the "/thr/gamow" part above with whatever path is appropriate for your machine. You will probably want to place $AMBERHOME/exe in your PATH.
2. Go to the $AMBERHOME/src directory, and create a link to the appropriate Machine file, e.g.

   ln -s -f Machines/Machine.hp MACHINE for HP, or
   ln -s -f Machines/Machine.sgi MACHINE for SGI, etc.
   

   (Note: To compile sander for SGI parallel machines, you will need to use Machine.sgi_mpi (for SGI's mpi libraries) or Machine.sgi_mpich (if you have installed MPICH).

3. Type "make". Loader warnings (especially on SGI -- see the Machine.sgi file) can generally be ignored; compiler warnings should be considered, but most are innocuous. If a program that you don't need initially fails to compile, you should consider commenting out that line in the Makefile, and seeing if the rest of the suite can be compiled correctly.
4. If you wish to use ROAR, do the following:

   a. go to the $AMBERHOME/src/roar-2.0 directory.
   

   
   b. edit the Makefile, to uncomment the lines appropriate
   for your machine.
   

   
   c. make install
   

5. To test the basic AMBER distribution, type "make test.all" in the $AMBHOME/test directory. Where "possible FAILURE" messages are found, go to the indicated directory under $AMBERHOME/test, and look at the *.dif files. Differences should involve round-off in the final digit printed, or occasional messages that differ from machine to machine (see below for details). As with compilation, if you have trouble with individual tests, you may wish to comment out certain lines in the Makefile, and/or go directly to the $AMBERHOME/test directory to examine the inputs and outputs in detail.

There is no automated test for gibbs with PME; if you are interested in this option, please look at the files in $AMBERHOME/test/sodium_gibbs_pme.

A note to users of earlier version of AMBER: The installation procedure is somewhat modified from earlier versions, as noted above, using the AMBERHOME environment variable and a master Makefile. All executable programs are installed in $AMBERHOME/exe; there is now no separate LEaP directory, and no need for a $LEAPROOT environment variable. The older programs prep, link, edit, parm, spasms and mdanal are no longer distributed with Amber, and have been placed into the public domain. Check the Amber web site for information about how to obtain these programs.