The ANATRA menu holds a set of options that allow you to analyse GROMOS
molecular dynamics trajectories. Since GROMOS does not use IUPAC nomenclature
and a non-IUPAC atom order, some synchronisation between the WHAT IF soup and
the GROMOS files needs to be done. You will therefore often be prompted
for the name of a GROMOS coordinate file and the corresponding molecule
in the soup. WHAT IF will align these two at the atomic level, and use
this alignment when reading the trajectory file. It is therefore of utmost
importance that you keep the corresponding trajectory and coordinate file
together.
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.
Large parts of the analysis software are written by B. de Groot (B.B-tje).
The command TRAGRA will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
You will be prompted for the residues to be followed, and this subset of
residues will be put in the movie option. Be aware that only 100 steps can
be displayed at once.
The command TRAGRL will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
You will be prompted for the residues to be followed, and this subset of
residues will be extracted from all selected trajectory steps, and put in
a mol-item.
The command TRACEN will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
You will be prompted for the residues to be followed, and this subset of
residues will be put in the movie option. You will also be prompted for
the atom on which to center the movie. All trajectories will be translated
such that this atom stays at the same spot. Be aware that only 100 steps can
be displayed at once.
The command FOLLOW will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
FOLLOW will follow the active atoms (see the USE*** commands) through a
trajectory file. Lines will be drawn that connect the subsequent positions
of these atoms in space. These lines will be put in a mol-item.
The command TRAGRA will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
You will be prompted for a residue and for the radius of the sphere
around this residue. This sphere of residues will be followed through the
trajectory and be put in the movie option. Be aware that only 100 steps can
be displayed per movie.
The command TRAHBO will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
You will be prompted for a residue and for the radius of the sphere
around this residue. All Hydrogen bonds within this
sphere of residues will be followed through the
trajectory and be put in the movie option. Be aware that only 100 steps can
be displayed per movie.
The command TRAGRA will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
You will be prompted for one atom. This atom will be followed through the
trajectory and its trajectory will be put in a MOL-item.
The command LOOPER will prompt you for the number of frames (should
not be larger than the number you sent to the screen with an
earlier TRA-like option). You will also be prompted for a mode,
cyclic or oscillating. In cyclic mode you see a jump everytime
at the end of the movie, because WHAT IF jumps back in one step
from the last frame to the first frame again, in oscillating mode
the direction of the movie is reversed every time the last or the
first frame is reached. Finally you will be prompted for the speed
of the movie. This number depends on the size of the movie, the
number lines/dots per movie step, and, of course, on your hardware.
So, you will have to experiment a bit with the speed. Normally numbers
between 1 and 10 are fine.
The option FOLLOW will follow activated atoms through a trajectory, and put
their trajectory traces in a MOL-item. You can use the USE*** options to
activate atoms.
The command USEALL activates all atoms in the soup for usage by
the FOLLOW option.
The command USECA activates all alpha carbon atoms in the soup for
usage by the FOLLOW option.
The command PARAMS will activate the trajectory analysis parameter menu.
The following parameters are available:
If you want, atoms can be pickable during a trajectory. Since, however,
the number of pickable atoms is limited, you can for long trajectories
of large molecules decide to only make the alpha carbons pickable.
If you give 0 only alpha carbons will be pickable; 1 makes
all atoms pickable.
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.
GROMOS gives default file names to all its files. To keep them apart, you can
add a project number to the options. (You see the two digits in the filenames
that contain the project number plus ten added to it). The command PROJEC
allows you to (re-)set the project number.
If you forgot how many steps there are in a trajectory file, you can use the
TRACNT option to count them.
The command ANADST will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
Then you will be prompted for two atoms. These two atoms will be followed
during the trajectory, and some statistics about their distance will be
given.
The command ANAVOL will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
Then you will be prompted for one atom. Some statistics about the volume
occupied by this atom during the trajectory will be given.
The command ANAHBO will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
Then you will be prompted for two atoms. If there is a hydrogen bond
between these two atoms, this hydrogen bond will be followed
during the trajectory, and some statistics will be
given.
The command TRARMS will like most ANATRA options prompt you for: A GROMOS
file name; The number of the corrsponding molecule in the soup; a trajectory
file name and the number of trajectory steps to skip between the trajectory
steps that should be used; The number of initial trajectory steps to be
skipped (the so-called warm-up phase).
Throughout the movie the RMS atomic displacement for the atoms in each
residue (with respect to the atoms in the soup) will be calculated, and
the plot of the RMS displacement as function of the residue number will be put in
the movie.
The command TRASCR allows you to run over a trajectory file, and execute a
script file on each step. Be aware that not all options can be used in these
script files. Also, it seems wise to save your SOUP before starting this option.
You might want to try the script file first on just the SOUP, rather than
immediately on the entire trajectory file.
Sometimes one atom of a covalently bound pair of atoms can move
across the boundary of the box. This will lead to stange long lines
that run all across the screen. To avoid this, you can use the
BNDCHK option. Be aware, however, that this costs extra CPU time.