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.
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:
Upon calling WADISC, the script will be initialized.
WADSSC will cause WHAT IF to show the script containing the options selected
so far, with their parameters.
WADEXE will execute all the commands in the script and analyze the results
(put the output either to the screen or the printer).
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.
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).
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
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.
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.
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.
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.
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.
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.
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.
WADDIH will count the number of phi/psi combinations per frame in an
unfavourable region of the Ramachandran plot as a function of time.
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.
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.
WADGRO will isolate one frame from the trajectory file and write it away
in GROMOS coordinate file format.
WADALL automatically executes and evaluates WADDIH, WADHBO, WADHST, WADRMS and
WADGYR.