58.1. A MORPHINE EXAMPLE

In the first and second worked examples we studied a protein Target (file PDB.pdb) which was supplied as ATOMS in PDB format. In the third example we studied gly.pdb which was HETATMS in PDB format. Now we will look at the morphine molecule in file morphine.cdb which is in Cambridge Data Bank Format.

Use your page editor to look at morphine.cdb. This file would be unacceptable as input to Programme GRIN which must have input files in PDB format. We must therefore use GREAT in order to change the format and the atom names.

Go from the your working directory in the Tutorial04 directory:

cd Tutorial04

Type Great as usual and start with GRIN.

Great (or type the full path as usual)

1

Enter morphine as the keyword in the intermediate menu and study MAIN MENU B.

morphine.cdb

Change item 1 to morphine.cdb, because the input file is actually called morphine.cdb (NOT "morphine.pdb").

You could also alter the name of the command file in Item 7. Call it "grin.morph.in" but DO NOT SUBMIT IT. Instead you should type PREPARE to prepare your command file "grin.morph.in" for submission later.

prepare

You will then be asked this unexpected question:

 Are there any Chlorine
 atoms in your file?

In fact Programme GREAT has found an atom called "CL1" and it is not going to guess if this is a chlorine or a carbon. You must give the answer YES because it is chlorine, which may come as a surprise with a morphine file. (It is of course the chloride counter-ion). You will be asked to check if this particular HETATM is really chlorine (It is), and will also be asked if there are any more chlorine atoms in your file. There are not.

You do want the HETATMS to "be renamed for use with Programme GRID", so answer YES to the next question. This will take a moment, and you may then be asked:

 Do you want this programme GREAT to guess
 most of the HETATM names? Answer GUESS or NO

Programme GREAT will try to decipher the MORPHINE.CDB file by itself if you answer GUESS (although it may occasionally have to ask you a question). It will ask you more questions if you answer NO, and you will therefore have more control over the final MORPHINE.PDB file which is produced. We suggest that you answer GUESS.

In fact GREAT will certainly have to ask you a question, because it finds that there are five separate hetero-molecules in your file. The input file MORPHINE.CDB actually contains one chloride counter-ion; one morphine cation; and three water molecules.

Almost certainly you do not want to study this mixture of molecules as your Target, so give the answer NO. You will then have the opportunity to rename each molecule, and to select the ones you want. This calls for clear thinking, because the morphine itself does not come first in the CDB file although it is the most important molecule.

Answer YES at this stage in order "to give each molecule an appropriate name", and then study the screen carefully. The first atom in the original MORPHINE.CDB file was the chloride counter-ion, and it appears as the first HETATM in your new PDB file. It is not a covalently bonded part of morphine, and has been classified as a separate molecule: "hetero-molecule MOL 5". You will be asked if you want to include this chloride ion as part of the Target, and should answer NO.

The next molecule is MOL 1 which is the morphine cation itself. It is "hetero-molecule MOL 1" and starts with HETATM 2. You will be invited to name it and can call it MOR. As you can see, the molecule name in a PDB file should be a 3-character code.

Finally you will be asked about molecules 2, 3 and 4 which are the three waters and should be rejected. Answer NO three times and your new PDB file will then be ready. The first lines of this new file will be printed to the VDU screen, so that you can check them. You can also enter a password if necessary for your copy of the Programmes. Otherwise just hit RETURN a couple of times, or type PREPARE or YES as appropriate.

The job will not be submitted at this stage, but the new command file will be PREPARED and so will a new copy of "morphine.cdb". In fact the morphine file will have been successively modified like this:

• First there was the original file in Cambridge format.

• This would be altered to a second file with all five molecules and the correct HETATM names. It would still be called morphine.cdb, but it would already be in PDB format.

• Thirdly there might be a morphine.cdb file in which the molecule name of Morphine had been changed to MOR, and the waters and chloride omitted.

These files will all be called MORPHINE.CDB (in small letters for Unix, and perhaps with generation numbers), although all the new files will actually be in PDB format. The latest file, which is the one that you want for input to Programme GRIN, will always be called MORPHINE.CDB (in small letters for Unix, without any generation number). This is exactly what you want, because you have already instructed Programme GRIN to take its input from a file with the name morphine.cdb (See above).

Now submit GRIN from the keyboard by typing:

Grin < grin.morph.in (or type the full path as usual)

and when that run has finished have a quick look at the output file: morphine.lout in order to be sure that there were no problems. Then type Great again in order to set up the GRID run.

Great

Hit GRID in MENU A and type the keyword morphine. We will use a different Probe this time, so answer NO and hit RETURN once or twice in order to reject the previous OH2 Probe.

In MAIN MENU J type the hidden keyword PROBE and you will go to MENU P.

probe

Hit item 3 in that menu and you will go to the first PROBE MENU.

3

We suggest that you try a phenolic hydroxy Probe so type OH and hit RETURN.

OH

Study the parameters which describe this sort of Probe. They have the following values and meanings:

1.650 is the Van der Waals radius of the OH Probe. 7.000 is the effective number of electrons in the Probe. 1.500 is the polarizability of the Probe. -0.15 is the net charge of the Probe. -4.50 is the maximum strength of a hydrogen bond made by the Probe. 1.400 is a reduced Van der Waals radius which is used if the Probe is making a strong hydrogen bond. 1 and 1 are the numbers of hydrogen bonds which the phenolic hydroxy Probe can donate and accept. 34 is the Type of the Probe. The "Type" is a number for a look-up table, and it defines hybridisation and hydrogen-bonding geometry of the Probe. Type is optional and may be omitted.

These nine parameters are considered in detail in the MD User Manual. However, the above definitions will do for now. Type YES to confirm that this is the Probe you want.

At this stage you should make certain that the GRIN run for morphine has really finished, because the output from GRIN will be the input to GRID. Then type the keyword ELSE to move to MAIN MENU J

else

and alter the name of the command file to grid.morph.in.

Finally type SUBMIT and proceed as before, calculating "all of the z-planes" in order to compute the whole GRID at once. Finish by typing ABANDON to get out of Programme GREAT while the morphine job is running in background mode.

You will now have done the GRID computations, and you should have the Grid map morphine.kont ready for studying on the Graphics.