59.1.1. Objectives

The aim of the present tutorial is to demonstrate the performance of the program Gmol2 for the transformation of mol2 formats in GRID-pdb format, and the use of the methodology reported in "Studying a set of Target" with GRID.

59.1.2. Working section

Change to the tutorial directory and list its contents.

cd Tutorial05

ls -l

In this directory we have included all the 20 molecules in Sybyl mol2 format. 3D molecular structures were build using CORINA followed by Energy minimisation with the Merk force-field as implemented in Sybyl 6.4. For this simple example all the molecules were built in their uncharged form. 3D molecular structures and the %HIA are reported below.

3D molecular structure	Name & symbol	Logit (%HIA)
	Alprenolol	1.1372
	Atenolol	0.0422
	Ciprofloxacin	0.3074
	Diazepam	1.2086
	Foscarnet	-0.7041
	Lactulose	-2.2321
	Mannitol	-0.4715
	Metolazone	0.2151
	Metoprolol	2.0086
	Nordiazepam	1.3936
	Olsalazine	-1.6413
	Oxazepam	1.2086
	Oxprenolol	1.2086
	Phenazone	1.2086
	Pindolol	0.9224
	Practolol	1.0746
	Raffinose	-2.5344
	Sulphasalzine	-0.8799
	Sulpiride	-0.2698
	Tranexamic acid	0.0591

59.1.3. Transformation of mol2 structures in GRID-pdb format

Prepare a file containing the list of the molecules:

ls -c1 *.mol2 > filemol2.list

Now, we should convert all the molecules from MOL2 into GRID-pdb format. This process is quite sophisticated, because GRID has to recognize the chemical types of atoms, distinguish between fixed and mobile hydrogens etc. ... This work is carried out by Gmol2 in automatic way.

Start the Gmol2 program:

gmol2 filemol2.list

Now Gmol2 will process all the 20 molecules one after the other. When the process is terminated, GRIN must be used to transform all the pdb structures in GRID-kout format. This conversion is fully automatic, but a command file is required to do the conversion and a list of pdb files is also required. In order to create the list, just type:

ls -c1 *.pdb > filepdb.list

Great will create the command file.

Great

Press 1 for GRIN and type filepdb in the intermediate menu. Change the menu 1 "filepdb.pdb" in "filepdb.list"

Give the path to "grin" and to "grub.dat" (please change according to YOUR GRID programme location) 

In [MENU] 4 put the path for "grin" program

/your_grid_directory/grin

in [MENU] 6 put the path for "grub.dat"

/your_grid_directory/grub.dat

Proceed to create the command file.

[MENU] 9

[MENU] 3

[RETURN]

Now, in the directory it has been created the GRIN command file grin.in. Run GRIN as usual:

Grin < grin.in &

After a few seconds some new files are created: .kout and .lout. The last file contains messages concerning the GRIN run.

GRID-kout files are now ready. In this final step we will create a GRID command file to process and produce automatically all the 3D interaction energy maps for all the 20 compounds.

ls -c1 *.kout > molecule.list

Great

[MENU] 2 (use of program GRID)

type molecule in the intermediate menu

[MENU] 1

change in "molecule.list"

[RETURN]

[MENU] 4

/your_grid_directory/grid

We will use a OH2 probe for the analysis, but up to ten probes can be used simultaneously.

probe

[MENU] 3

OH2

yes

We will change the format of the output file in binary, and the grid spacing at 0.5A

LIST

-2

NPLA

2

And instruct the program to prepare the command file

[MENU] 9

[MENU] 3

tutorial test

[MENU] 1

[RETURN]

[MENU] 7

The command file is now prepared.

Run GRID now

Grid < grid.in &

After a three or four minutes we obtain the output files, molecule.kont and molecule.lont. GRID has calculated the interaction between a water molecule and our molecules at a large number of grid nodes (about 120000 for each probe). As we did not define explicitly the cage size, GRID has used a cage large enough to enclose all the compounds. The default grid space of 1 Å was changed at 0.5Å to produce better interactions estimation. All these interactions are, in binary format, into the molecule.kont file.

59.1.4. 3D MOLECULAR INTERACTION FIELDS VISUALISATION

In order to visualise the MIF together with the molecular structures, follow the usual options:

Gview molecule.kont

A window appears with yellow region. Make it bigger by clicking in the square icon in the upper right corner. Yellow points represent negative interaction energies (favourable).

To change the energy levels, select:

Edit->Field style

Move the cursor of the interaction energy levels up to -3.5 and then press Exit on the dialogue box. To change the molecule's style, press:

Edit->Molecule style change the Rendering style to "Sticks". Then press Exit

Move the image pressing the left button of the mouse and moving the mouse at the same time.

Move the image pressing the left button of the mouse and moving the mouse at the same time.

Gview automatically displays the KOUT structures with the associated MIF for the selected probe and, since the GRID kont file contains more than a molecular structure, you can use Gview to browse the structures and the MIFs in the graphic window:

Edit->Select

Click on tab called "Field", scroll down the below listed molecules and then click Exit.

For more information about Gview setting click here.

The produced MIFs can be correlated to a complex biological response, through useful molecular descriptors from a computational procedure called VolSurf. Using PLS, available in the VolSurf package ( http://www.moldiscovery.com/soft_volsurf.php), the Human Intestinal Absorption %HIA of this series of molecules ca be related to the GRID MIF obtained from water and DRY probe (the DRY probe was not used in this example).

Typical example of correlation is reported in the Figure above, where the experimental data are reported against the calculated one obtained from VolSurf in the GRID Molecular Interaction Fields.

Summing up, the MIF maps can be easily generated, they are easily interpreted in terms of molecular structure and are very suitable both for designing test sets and for quantitative structure-property modelling.

You have now completed your seventh Tutorial. Well done!! We look forwards to hearing from you if we can help in any way.

Please, continue with Tutorial 06.