Analysis of the results

 

In this section you will run several scripts to extract the energy and structural information from your conformation files. These will give you the energies and structural deviations of the families of structures that have been generated. The structures are struc11, struc12, struc13, ... struc251. There one hundred structure files in all with in loop counter from 1 to 25 and outer loop counter from 1 to 4.

We will be interested to compare those that have run with restraints to those that ran without restraints.

Once the job is complete you can analyze the results using theenk_output, enk_energy and enk_rms BTCL scripts. These scripts have been written to extract the energy of the conformations and to describe their statistics. They can be run under DISCOVER3 in the same directory that has output from the 100 ps of production dynamics. They will sort through the output and history files of the 100 minimized structures in order to obtain information on the distribution of energies of the structures. Before you begin to run these scripts you will need to delete some text in the mdf file. First copy your car and mdf files to the names enk.car and enk.mdf.

Then use the vi editor to modify enk.mdf. Find the text #atomset using the / command. Type in

The next 29 lines contain statements that look like

@quartet torsion *:*_*:chi1

N CA CB CG

Etc.

These lines are a problem for the script and the red labeled text above needs to be deleted from the file. Delete these lines by typing 29dd in the vi editor (while you are on the line that contains #atomset. Note that you still must have the #end marker that tells the program where the end of the molecular data file is. Following these instructions should delete all of the lines except #end.

 

Generating a list of energies and properties of structures

 

The scripts have been written for you, but you may need to modify them.

 

Interactive execution of a script (you may skip this part).

To execute a script run discovery in interactive mode:

You will see the BTCL prompt. At the prompt you must first define the files that will be used to obtain molecular data. You do this by setting the PROJECT. For example, if your car and mdf files are named enk then you type

BTCL> set PROJECT enk

enk

BTCL>begin

 

INPUT FILE

----------------

 

File type Name

------------ --------

Forcefield /usr/local/apps/msi/970/irix6m3/biosym_lib/cvff.frc

Molecular data enk.mdf

Coordinate enk.car

 

Now you need to open a file to write the results of your analysis. For example, for the analysis of energies and root-mean-square deviations of the structure you will use the script enk_output. To open an output file for writing type

BTCL> open enkoutput a

file4

Discover3 has defined file4 as the file for writing. In the script file4 will be referred to as the file for putting the output.

Then you can use the more editor to observe the commands in the script enk_output by typing

You can select text using the left mouse button and then place in the BCTL prompt using the middle mouse button (while in insert mode in the vi editor). This is a standard cut and paste method in the UNIX operating system.

 

Setting up a script for batch mode (this has been done).

Instead of doing this you can add the above lines to the script and use redirect. Type

Then use the i command (for insert). Type in the following lines

set PROJECT enk

begin

open enkoutput a

at the top of the file and use Esc :wq to exit. Now run DISCOVER3 with redirected input

Either way the file enkoutput that you create should have the energies and rms deviations of the structures.

 

Generating a list of rms deviations of structures

 

A similar procedure is followed to generate a list of the root-mean-square deviations of the structures from the minimum energy structure. Your output consists of 100 or more structures in files labeled struc11, struc21 etc. The enkoutput script has lists the energies. Because of problems with formatted input it is easier to use the enkenergy output file generated by the script enk_energy. This output file is just a list of energies in order of the file listing (struc11, struc12, .. through struc251). You must use that output to find the minimum energy structure. You can do this by inspection or using a spreadsheet or using the programs energy_bin and find_min.

The program find_min can be downloaded and compiled

at the command line on the computer. The program findmin operates on enkenergy and enkfile output files.

Once you have identified the minimum structure you will need to edit the enk_rms script. Change the name of the reference file for the minimum energy structure. The default reference file is struc11.cor. Typically, you will find a different structure with minimum energy for comparison. Enter the name of this structure into the enk_rms script and save it. Then run the enk_rms script using redirect.