grid saves information about the steric and electrostatic environment at each point on a grid, so that ligand orientations can be scored rapidly during a dock run.
You determine the location and dimensions of the region to be gridded by using the program showbox to create a box which contains the desired region. For grid, the box should enclose the volume that the ligand orientations are likely to occupy. An easy way to accomplish this is to generate a box which encloses the spheres to be used for docking along with an extra margin. The box generated should be viewed along with the receptor and possibly regenerated until it looks good.
First read the receptor PDB file into a text editor. Remove all waters and complexed ligands. Special attention should be given to the names of atoms at the termini and the residue names for histidine and cysteine. You will need to rename each histidine residue depending on the protonation state you want to assign it: hip for positively charged (hydrogens on both nitrogens), hid for neutral with the delta nitrogen protonated, and hie for neutral with the epsilon nitrogen protonated. cys refers to a cysteine with a free sulfhydryl group; cyx refers to a cysteine involved in a disulfide bond (a half-cystine). Note that some structures in the pdb use cys in disulfides; these should be edited to cyx.
Second the user must construct a SYBYL MOL2 format of the receptor which includes sybyl atom type and partial charge assignments. We routinely use sybyl for this task, but other modeling packages can be used provided you have a way to convert the resulting receptor file into MOL2 format. The following instructions will apply to the use of sybyl for this task.
In sybyl, activate the BIOPOLYMER menu from the OPTIONS menu. From the BIOPOLYMER menu, select BROOKHAVEN READ to read in the receptor PDB file. A dialogue box will ask if you want to center the molecule. If you need to retain the reference frame of the receptor (e.g. for consistency with other collaborators) then don't center the coordinates. Instead, you will need to manually find the receptor since it will probably not appear on the screen. Hit the lower button on the left side of you sybyl window which looks like a molecule surrounded by arrows. In the small window that appears, hit the button called "reset extents." Now you should see the receptor from a distance. Use the far right mouse button to rotate the receptor to its highest point on the screen. Use the middle mouse button to translate it to the center of the screen. Then use the combination of mouse buttons to zoom in on the receptor. You may need to rotate it up and translate back to the middle a few times to keep it from escaping the window. You will need to repeat this exercise every time you read in any molecule that is in the unperturbed frame of reference of the receptor (i.e. bound ligands).
Check if all of the atoms were identified properly by sybyl. You can label problem atoms by selecting LABEL ATOMS. In the atom selection window, press the SET button. If you see a set type called "Unknown Atoms" then select it. Any atoms that were not recognized by sybyl will now be labelled. This most often occurs with oxygen atoms at the C-terminus, with unusual amino acids, or if cofactors or ligands were not removed. If the terminal carboxyl oxygens are the problem, then rename them with the text editor and reread the receptor. For other problem atoms you will need to consult the sybyl manual.
Next, you should model in any incomplete residues. Check the original PDB file for a list of residues whose density was to weak to model completely. If no list exists, then check the total charge on each residue as reported by grid when you run it later; if some residues have non-integer charges, then you may need to come back to sybyl and model them in. To do this, identify the residue to fix. From the BIOPOLYMER menu, select MODIFY, then MUTATE RESIDUE. Click on the residue you want to modify, then select which type of residue you want to mutate it to (use the same type of residue).
Add hydrogens by using the BIOPOLYMER menu option. It is important to add ALL atoms, not just POLAR atoms, since grid needs them to identify VDW atom types. Load charges from the BIOPOLYMER menu. You may use ALL atom or UNITED atom KOLLMAN charges. Write out the receptor to a MOL2 file by using the write option in the FILE menu.
Input to grid is interactive. Just type grid -i grid.in to launch it. All input parameters will be saved in the file called grid.in. After all parameters have been input, hit CTRL-C to kill the job. Relaunch it in background mode by typing grid -i grid.in -o grid.out&.
All recommended parameter values will be suggested by grid when run interactively, but here are a few suggestions. grid_spacing values between 0.2 and 0.5 are recommended; fine grids are preferred if there is sufficient memory in the computer. Any combination of grid point spacing and box size can be used, but it is recommended that about a million total grid points be used. Of course this value depends on memory resources.
A dielectric function of 4.0r or 4.5r and a cutoff of 10.0 Angstroms or more are appropriate in most cases. (This dielectric corresponds to specifying distance_dielectric yes, dielectric_factor 4 or 4.5, and energy_cutoff_distance 10.) If a constant dielectric is selected, an "infinite" cutoff (one large enough to include the whole receptor) should be used.
It is important to check the residue charges that are output by grid. If any non-integer charges are reported, then some residues may have improper charges assigned to them, or they are not completely modeled in the input file. If no charged residues are reported, then check to make sure that charges were properly loaded in the input file.
Four output files, named grid.bmp, grid.cnt, grid.chm, and grid.nrg, will be produced which hold the bump grid, contact grid, chemical grid and force-field grid, respectively.