ANALYZE TRAJECTORY (ANATRA)

Introduction.

The option ANATRA brings you in the menu from which you can do all kinds of analyses on Molecular Dynamics trajectories produced by the simulation package GROMOS, which, if you have the license, is delivered with WHAT IF and is present in WREGRO.

The way to analyse the trajectory is chosen by the user, but WHAT IF requires a certain input. WHAT IF needs a GROMOS coordinate file (containing also atom names etc.) named WEDAVPGRO10.DAT and a trajectory file WEDFITCRD10.DAT. These are files produced by the program WEDTRA, and if these files are not present in the the directory from which WHAT IF is run, WHAT IF will ask for the 'raw' GROMOS output and run WEDTRA to create these files. Once WEDTRA has been run, the user can select from a dozen or so options representing properties that can be followed during the trajectory.

Initializing the setup of the anatra menu (WADINI)

The first thing WADINI will ask is if you want to use the grafical interface of WHAT IF or not. Selecting the grafical interface will pop up a graphics screen with your molecule after typing for instance WADDIS. Subsequently, two atoms can be clicked between which the distance will be monitored as a function of time in your trajectory. If the graphical interface was not selected, WADDIS will prompt you for the two atom numbers between which the distance will be monitored.

Typing WADINI in the ANATRA menu will initialize the anatra menu, and check if the files required by ANATRA are in your current directory. If you have performed your simulation with WHAT IF, and did the trajectory handling step WEDTRA from the essdyn menu, these files will be present. If the files can not be found by WHAT IF, you will be asked for the names of the input files required. If some processing still needs to be done, WHAT IF will automaticcaly run WEDTRA to provide the proper files.

ANATRA works as follows: After WADINI has been run, you can select any number out of the options present in the ANATRA menu ( they are saved in a script-like manner). WHAT IF will remember all selected options, and when WADEXE is selected, all trajectory evaluations will be executed. Upon calling WADINI, all previously executed commands will be removed from WHAT IF's memory, which also occurs at calling WADEXE.

The options to choose from are:

Initializing the script (WADISC)

Upon calling WADISC, the script will be initialized.

WADSSC (shoing the script)

WADSSC will cause WHAT IF to show the script containing the options selected so far, with their parameters.

Run the script (WADEXE)

WADEXE will execute all the commands in the script and analyze the results (put the output either to the screen or the printer).

Evaluate the results of a previous run of the script (WADANA)

If you want to visualize the results of (a previous run of) the script (again) you can select WADANA. It will give the same output as WADEXE, only not execute the program to generate the data again.

Using DSSP to evaluate geometrical properties (WADSSP)

WADSSP selects DSSP (if available, i.e. if you have the license, it is not part of the WHAT IF package...) for the calculation of the geometrical properties ACC (total solvent accessible surface), HST (secondary structure assignments), and HBO (the total number of main chain - main chain hydrogen bonds). For the latter two, also DSSP independent options have been written (WADHST and WADHBO). However, note that these options have not been well tested and only provide qualitative data. Therefore we suggest that you only use them for fast experiments (they are considerably faster than DSSP) but not for any quantitative needs.

The result of WADSSP is the creation of four files in your directory. Only the options selected in the script are automatically visualized by WHAT IF after using WADEXE (so, for instance, if your script only contains the commands WADSSP and WADHBO, only the output of HBO (the number of hydrogen bonds) is evaluated after WADEXE. ACC and HST are calculated without any extra cost as well, only not visualized).

Following the secondary structure as a function of time (WADHST)

Depending on the WADSSP flag (see WADSSP) secondary structure assignments during the trajectory will either be calculated by the program DSSP or by an approximation that is less accurate but a lot faster. selecting WADHST will produce two kinds of output:

1) it counts the number of residues in random coil conformation as a function of time

2) it produces a map of all secondary structure as a function of time

Following a inter atomic distance through time (WADDIS)

Depending on the selection in WADINI for the graphical interface, the user will either click two atoms on the screen between which the distance will be monitored in the trajectory or type the atom numbers of the two atoms.

Following an angle through time (WADANG)

Depending on the selection in WADINI for the graphical interface, the user will either click three atoms on the screen between which the angle atom 1 - atom 2 - atom 3 will be monitored in the trajectory or type the atom numbers of the three atoms.

Following a torsion angle through time (WADTRS)

Depending on the selection in WADINI for the graphical interface, the user will either click four atoms on the screen between which the torsion angle atom 1 - atom 2 - atom 3 - atom 4 will be monitored in the trajectory or type the atom numbers of the four atoms.

Following a hydrogen bond through time (WAD1HB)

Depending on the selection in WADINI for the graphical interface, the user will either click three atoms on the screen (donor, hydrogen, acceptor) or type the atom numbers of the three atoms, and WHAT IF will calculate the percentage of time that a hydrogen bond is formed by these three atoms. On the basis of this, WHAT IF will decide if a stable hydrogen bond was present at this position or not. WHAT IF uses the hydrogen-acceptor distance and the donor-hydrogen-acceptor angle to decide whether a hydrogen bond is present or not. It generates a number that is some kind of stability measure for a hydrogen bond. the larger it gets, the more unstable the hydrogen bond is.

Following a phi/psi angle through time (WAD1PP)

Depending on the selection in WADINI for the graphical interface, the user will either click a residue on the screen or type the residue number of the residue of which the phi/psi angles will be monitored. The result is presented in a ramachandran plot, where phi is ranging from -180 - +180 degrees along the x-axis and psi is put along the y-axis.

Following the radius of gyration as a function of time (WADGYR)

Selecting WADGYR will produce a plot of the radius of gyration of the simulated protein as a function of time. It is a measure of the compactness of the protein and it should not increase too much duing your simulation. When it does, this is usuallly a sign of the first stages of unfolding of a protein.

Following backbone-backbone hydrogen bonds as a function of time (WADHBO)

Depending on the WADSSP flag (see WADSSP) hydrogen bonds between backbone atoms are monitored either by DSSP or by an approximation that is less accurate but a lot faster.

Following dihedral angles as a function of time (WADDIH)

WADDIH will count the number of phi/psi combinations per frame in an unfavourable region of the Ramachandran plot as a function of time.

Following solvent accessible surface as a function of time (WADACC)

WADACC evaluates the total solvent accessible surface of each frame as a function of time. Now, WADACC only works in combination with WADSSP. Somewhere in the future, also a DSSP independent (ans faster) calculation of ACC will be available.

Calculating the RMS of positional fluctuations (WADFLC)

WADFLC calculates the rms of the atomic fluctuations of the atoms. This is a very crude measure to find out in which part of the protein the motion is concentrated.

Isolating one frame out of a trajectory (WADGRO)

WADGRO will isolate one frame from the trajectory file and write it away in GROMOS coordinate file format.

Do most of the fast-to-check overall analyses (WADALL)

WADALL automatically executes and evaluates WADDIH, WADHBO, WADHST, WADRMS and WADGYR.