INSTRUCTIONS FOR THE VIBRATIONAL ANALYSIS TUTORIAL
SINGLE M13 STRAND (SEQ OF 50 AMINO ACIDS)

This tutorial will demonstrate how to set up a
system to run a vibrational analysis simulation
of a medium sized peptide with implicit water
parameters.

The goal here is to find Omegas of the Dynamical
Matrix that are less than 30 cm-1.  To do this
we use the phonon functional (ORDER N Methods)
for finding only the smallest eigenvalues of the
dynamical matrix.

There are 3 main steps that need to be followed.

1) Create Saguaro parameter, coordinate, and molecule files
2) Minimize the structure
3) Run Vibes

After step 3, the output file will contain the set of lowest
eigenvalues and there relative errors and the trajectory
file will contain the EIGNEVECTORS OF THE DYNAMICAL MATRIX.

If you wish, you can then analyze the eigenvector data file
by using the dispvector tool. The dispvector tool creates
a XYZ file with vibrational displacements sutible for ploting.

STEP 1
This can be performed in three ways:
1) create parameter files "by hand" (NOT RECOMENDED)
2) use xleap GUI in AMBER to make amber top and crd files
   then convert to saguaro using Amber2saguaro.x tool
3) use pepalyze or... if you simply want generic parameters
   (no charges just a few standard springs and VDW parameters)
   use GenericP.x

Parameter, coordinate, and molecule files have already been created
for you .... they are m13.parm m13.gf2k and m13.mol

STEP 2
1) First get (or make) an options.in file that specifies what
   options you will be running for the simulation
   This file has been created for you .... optmin.in
2) Run Sagauro.x The command to use here is:

   Saguaro.x -i optmin.in -p m13.parm -c m13.gf2k -m m13.mol \
             -r m13_min.gf2k -e m13_min.ene -o m13_min.out

   The -r tells Sagauro to put the final structure coordinates in the
   file m13_min.gf2k for restarting later and the -e is to specify
   the energy file, the -o is for the output file.
   The output file contains all information about the simulation
   and any errors that may have occured during the execution.

   NOTE!! THE FILE m13_min.gf2k HAS ALREADY BEEN CREATED

STEP 3
1) First get (or make) an options.in file for the vibrational analysis procedure.
   This file has been created for you .... optvibe.in
2) Run Saguaro.x The command here is:

   Saguaro.x -i optvibe.in -p m13.parm -c m13_min.gf2k -m m13.mol \
             -r m13_vib.gf2k -x m13_evec.gf2k -o m13_vib.out

NOTE!! The restart file specified (m13_vib.gf2k) is junk and can be
       deleted

The output file contains information on the number of Dynamical Matrix
times vector operations were required and also contains the list of
lowest eigenvalues found.

The trajectory file (specified by -x) contains the corrisponding 
eigenvectors of the Dynamical Matrix.

To form the DISPLACEMENT vectors, simply run Dispvector.x and follow
the prompts.  This program will create a XYZ format file that
can be used in a program (such as JMOL) to visualize the vibrations.

ECD 3/12/07

END TUTORIAL
