Introduction to SYBYL

GETTING STARTED:

1) The instructor will provide you with student accounts and passwords. These accounts will remain active for the duration of the course.

 

2) Log onto the SGI workstations with your account and password

 

3) Materials for the training exercises will be available in the directory "exercise1".  To access this directory, type the following command at the command prompt:

·   cd exercise1

and hit [enter]

 

4) For these exercises, you will be using the SYBYL suite of software.  To run SYBYL, type:

·   sybyl

and hit [enter]

 

EXERCISE 1:  MOLECULE BUILDING USING SYBYL

In this exercise you will be asked to draw and save the following molecule:

 

molecule structure

 

1) To begin, locate the {Build/Edit} button on the top bar of the SYBYL interface and click it.

 

2) On the pull-down menu, you will see a button for {Sketch Molecule...} -- click that too.

Note:  in the future, I will use the following shorthand notation:

*   {Build/Edit} >> {Sketch Molecule...}

to simplify the description of steps like 1) and 2)

 

3) SYBYL can handle as many as 10 different molecules in memory at any given time.  It does this by storing the different molecules in bins called "Molecular areas" numbered M1 through M10.  SYBYL is asking you which Molecular area you would like to use for your first molecule.  M1 is highlighted by default.  Simply click {OK} to select M1.

 

4) You now have the three widgets used for building molecules.  On the middle widget, click the {Draw} button.  You are now ready to being drawing.

 

Here are some hints for drawing:

*  In "Draw" mode, every time you click on the black screen, you will draw an atom

*  If the atom is enclosed in a small yellow square, it means that the next atom you draw will form a bond to the atom with the yellow square

*  If you do not want your next atom to be bound to the atom with the yellow square, click inside the yellow square and it will go away

*  If you want your next atom to be bound to an atom that does not have a yellow square around it, click on the atom you want to bind to and that will give it a yellow square

*  If you want to form a bond to two already existing atoms, simply click the two atoms in succession

*  If you want to form a multiple bond between two atoms, click on the two atoms in succession again

 

5) Begin inputting atoms where you would like to see them in your molecule.

Note:

*  When you first input your atoms, they will all be Carbon by default.  Leave them that way for now -- it will be easier to change them from Carbon to other elements later than it will be while you're sketching.

*  You should not bother drawing in any atoms that will correspond to Hydrogens when sketching.  Hydrogens can be added automatically later.

 

6) Sketching molecules can be tricky and many people end up with a few bonds that they did not intend to sketch.  If you would like to delete such spurious bonds:

·  go to the middle drawing widget and click {REMOVE_BOND}

·  click on the two atoms whose bond you wanted to delete

Note:

*  as soon as you click {REMOVE_BOND}, you are no longer in "Draw" mode -- you are in "Delete Bond" mode and will keep on deleting bonds with every click until you get back to "Draw" mode.

*  to get back to "Draw" mode, go to the middle drawing widget and click {Draw}

 

7) If you have any extra atoms that you don't want:

·  go to the middle drawing widget and click {REMOVE_ATOM}

·  click on the atoms that you would like to delete

·  don't forget to go back to "Draw" mode when you are done deleting!  Otherwise you will continue to delete atoms

 

8) Once you have placed atoms corresponding to all of the heavy atoms in flavopiridol, and have the right bonds between all of them, you are  ready to give them the right atomic type.

·  Flavopiridol has 3 Oxygen atoms.  In order to change atoms from Carbon to Oxygen, click on the {O} in the bottom widget and then click on each of the atoms you would like to change.

·  Do the same for the Chlorine and Nitrogen atoms.

 

9) You are now ready to add H's.  To do this, simply go to the middle widget and click on {ADDH}.

Note:

*  if you have made any mistakes in specifying your bonds (e.g., drawing a single bond where you wanted a double), you will get the wrong number of Hydrogens.  Check your structure carefully.

 

10) There are numerous other molecular drawing options in the sketch tool.  These are described in detail in the online documenation that comes with our Tripos license.  To access this online documenation, minimize your SYBYL window, click on the Netscape icon, and find the Bookmark entitled {Sketcher Menu Items}. 

 

11) For now, however, let's exit the molecular sketcher by clicking the {Exit} button on the middle widget.

 

12) You now have your molecule alone on the black screen.  You can look it over carefully by manipulating it in the screen using your mouse.      Specifically:

·  if you hold down the right mouse button and move your mouse, you will rotate the molecule

·  if you hold down the middle mouse button and move your mouse, you will translate molecule

·  if you hold down both the middle and right buttons you will focus in, or pan away from the molecule

 

13) If you notice any serious chemical errors (incorrect atoms or bonds) in your molecule, go back to the sketcher as follows:

·  {Build/Edit}  >>  {Sketch Molecule}  >>  select M1  >>  {OK}    and make the relevant corrections.

 

14) In step 12 you probably noticed that the molecule does not have the proper three dimensional structure.  To correct this, you are going to need to do a geometry optimization as part of the next tutorial

 

EXERCISE 2:  GEOMETRY OPTIMIZATIONS USING CLASSICAL MECHANICS

In this exercise, you will optimize the structures of two different molecules -- flavopiridol and taxol:

1) Starting the with flavopiridol molecule you sketched in Exercise 1,

   bring up the minimization widget as follows:

·  {Compute}  >>  {Minimize...}

 

2) The default settings for SYBYL's classical mechanics optimizer are very good for straightening out the three dimensional structures generated by the molecule sketcher.  So, without changing any settings, simply click {OK}.

 

3) The molecule will optimize fairly quickly.  Once it is done, check it over to convince yourself that the three dimensional structure looks more sensible now.

 

4) In case you need the flavopiridol molecule later, you should save it as follows:

·  {File}  >>  {Save As}

·  in the {File:} box, enter the name "flav.mol2"

·  select m1  >>  {Save}

 

5) Now that you have saved your flavopiridol work, you may delete the molecule from SYBYL as follows:

·  {Build/Edit}  >>  {Zap (Delete) Molecule}

 

6) You are now going to optimize a more complicated molecule -- taxol.  In this case, you will not have to sketch taxol by hand because there is already a crystal structure available for the molecule.  You can load this structure as follows:

·  {File}  >>  {Read...}

·  click on "1JFF.pdb" from the list of files

·  select m1

·  click {NO}  (do NOT center the molecule}

 

7) What this gives you is the entire crystal structure for taxol docked in the protein tubulin.  For now you will not need tubulin, so you will need to extract taxol from the crystal structure.  Bring up the "Extract" widget as follows:

·  {Build/Edit}  >>  {Extract...}

 

8) On the widget, click {Substructures}

 

9) This gives you a "Substructures" widget.  Scroll down this widget all the way to the bottom and you see the Taxol moiety.  Click on {TA1839} and click {OK}.

 

10) From the main "Extract" widget do the following:

·  {OK}  >>  select M2

 

11) At this point, you will have extracted taxol from tubulin and stored it in a new molecular area.  To get rid of the unwanted tubulin:

·  {Build/Edit}  >>  {Zap (Delete) Molecule}  >>  select M1

 

12) If the whole screen appears to have gone blank, don't worry!  The taxol is probably still in there, but is just outside of the viewing area.  To find it, use your mouse to pan out.  I.e., hold down both the middle and right mouse buttons and pull the mouse towards yourself.

 

13) Once you've found the taxol, try to center it with your mouse.  Once it's centered, try rotating it around.  If it keeps sliding way off to the side when you rotate, you will need to make the molecule's center of rotation coincide with the center of the screen. To do so:

·  rotate the molecule with the right mouse button until it is far from the center of the screen

·  translate the molecule (middle mouse button) back into the center of the screen

At this point, the molecule's center of rotation should be closer to the center of the screen. It may still not be perfect -- if not then repeat the two steps above until you have it pretty well centered.

 

14) The molecule may be colored monochromatically at this stage.  In order to be able to see the different atom types:

·   {View}  >>  {Color}  >>  {By Atom Type}

 

15) When you bring up a molecular structure straight out of a PDB file as you have in this case, SYBYL doesn't always get all of the bonds described correctly.  Check the structure over to see if you see anything out of the ordinary.  One big problem you should see is the bonding in a six-membered ring that (if you know the taxol structure) you know should be a phenyl ring.  To correct this, bring up the "Modify Atom" widget as follows:

·  {Build/Edit}  >>  {Modify Atom}  >>  select "ONLY_TYPE" 

 

16) You will need to specify the atoms that currently have incorrect bonding behavior.  To do this, reorient the molecule so that you have a good view of the incorrectly bound phenyl ring, click on each of the 6 Carbon atoms in the ring (they will become highlighted with little green diamonds) and then click {OK}.

 

17) You are now prompted for the type of atom you want to change each of these Carbons to.  For a description of each of the different SYBYL atom types, open up your Netscape browser and choose the {Atom Types (Tripos)} bookmark.  For now, though, you are going to want to change all of these carbon atoms to 'aromatic carbons'.  To do so, scroll down on the widget, select "C.ar" and hit {OK}.

 

18) There are two more atoms that need to be modified. To see which ones, generate labels for all the atoms as follows:

·  {View} >> {Label} >> {Atom Id...} >> select M2 and click {All} >> {OK}

 

19) Observe that atom "44" (a carbon) currently has 5 bonds. The double bond between that C (44) and N43 is incorrect -- it should instead be a single bond. Change N43 from N.2 to N.am (amino) and change C (44) to C.2.

 

20) At this point, you will have changed the first of the six C atoms.  The widget is now asking you is you want to change the second atom to "C.ar" as well (note where the green diamond is on the molecule to see which atom you're about to change).  You do wish to change this one to "C.ar" as well so click {OK}.  In a similar fashion, the widget will cycle through all of the atoms you've asked to change and will disappear when you're done.

 

21) You are going to need to hydrogenate your structure in order to optimize it properly.  To do so:

·  {Build/Edit}  >>  {Add}  >>  {Hydrogens}

 

22) You are now ready to being an optimization, so first save your structure:

·  {File}  >>  {Save As}  >>  choose "m2"   >>  call the molecule "taxol_start.mol2"  >>  {OK}

and then bring up the Minimize widget as follows:

·  {Compute}  >>  {Minimize...}

 

23) This time, we are not going to use just the default settings.  We would like to try to reproduce some interesting experimental results that suggest that there is an observable attraction between one of the two phenyl rings close to each other in the taxol crystal structure with the third phenyl ring on the other side of the taxol molecule.  To try to reproduce this, we are going to:

·  change the maximum number of optimization iterations (in the widget's "Max Iterations:" text box) from 100 to 1000

 

24) We are also going to make the interaction forces more realistic as follows:

·  click the {Modify...} button next to "Energy Setup" to give you the Energy Setup widget

·  on this new widget, click the button next to "Charges" that currently says {None}.  Change it to "Gasteiger-Huckel".

·  since the two phenyl rings of interest are currently more than 8.0 Angstroms away from each other, change the "NB Cutoff:" text box from "8.0000" to "15.0000".

·  Click {OK}

 

25) Submit the job by clicking {OK} on the minimize widget.

 

26) When the job is done (in a few minutes), compare it to your starting structure by loading the starting structure back into SYBYL:

·  {File}  >>  {Read...}  >>  select "taxol_start.mol2" from the "Files:" list and select "m1" as the molecular area  >>  click {OK}

 

27) To make it easier to compare the two structures, you might wish to recolor the starting structure:

·  {View}  >>  {Color}  >>  {Atoms...}  >>  select M1 and click {All}  >>  {OK}

·  choose a color from the list (purple is often good)  >>  {OK}

 

28) Make a note of the qualitative differences between the initial and final structures. Compare the relative energies by looking them up within the text window at the bottom of the page. The final energy should be right at the end of the optimization, in the line that reads:
            “Optimization completed, Total Energy :"
while the initial energy is right at the top of the optimization (you will need to scroll way up using the window's side bar) in the line that reads:
            "Total Energy :"

 

OTHER THINGS TO TRY: 

Constructing proteins:  inputing a specific sequence of EPSP synthase

1) {Build/Edit}  >>  {Zap (Delete) Molecule}  >> {All}  >>  {OK}

2) {Biopolymer}  >>  {Build}  >>  {Protein...}

3) select:  {ASN} {ALA} {LEU} {THR} {ALA}

4) for "Conformation" select:  "alpha_helix"

5) {Build}

6) {Biopolymer}  >>  {Build}  >>  {Protein...}

7) for the connection point, select "M1(A/ALA5.C)"

8) select:  {LEU} {GLY}

9) Conformation: "turn1"

10) {Build}

11) {Biopolymer}  >>  {Build}  >>  {Protein...}

12) connection point:  "M1(A/GLY7.C)"

13) select:  {VAL}

14) leave Conformation as "None"

15) {Biopolymer}  >>  {Build}  >>  {Protein...}

16) connection point:  "M1(A/VAL8.C)"

17) select:  {SER} {TYR} {THR} {LEU}

18) Conformation: "beta_sheet"

 

Analyze secondary structure:  ribbon structure for entire EPSP synthase enzyme

1) {Build/Edit}  >>  {Zap (Delete) Molecule}  >> {All}  >>  {OK}

2) {Biopolymer}  >>  {Brookhaven File}  >>  {Read...}  >>  "M1:"  >>  {OK}

3) select "eps.pdb"  >>  {OK}

4) select:  "Center the Molecule"  >>  {OK}

5) {Biopolymer}  >>  {Assign Secondary Structure...}  >>  "M1:"  >>  {OK}

6) to remove the molecular structure so you can just see the ribbon drawing, click on the following sidebar button:

check boxes

7) in the small widget that pops up, click on the button indexed by "Mol Display" (column) and "D1" (row).

EXITING:

1) {Build/Edit}  >>  {Zap (Delete) Molecule}  >> {All}  >>  {OK}

2) {File}  >>  {Exit SYBYL}


CONTACT
David Johnson
emaildkjohnson@ku.edu
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