The still molecule (.grd, .vol) files

Step 1: Preparing the PDB file:

The complete description of the still molecule includes two files that must be generated before running DOT:

the electrostatic potential field of the still molecule (.grd file), and

the solvent excluded volume of the still molecule (.vol file).

Typically one starts with a Protein Data Bank (PDB) file which does not have hydrogen atoms. Since DOT models intermolecular hydrogen bonds as electrostatic interactions, it is important to add the hydrogen atoms to the protein. This addition can be accomplished by using a program such as Insight II by MSI. The "Modify" function in the Biopolymer module of Insight will add all of the hydrogen atoms to the protein. This is also a good opportunity to adjust the charges of specific residues such as histidine. The protein should then be saved in PDB format with the hydrogen atoms.

Also, some PDB files have alternate locations for given atoms. These duplicate locations are marked with 'A', 'B', 'C', ... in the PDB file. In order to use such a PDB file with the DOT utilities, you must choose exactly one of the alternative locations, deleting the others, and replace the 'A' or 'B' marker with a space character.
Since the file-preparation utilities described below (such as UHBD) use a different atom-naming convention than Insight does, the hydrogen-appended PDB file must be translated using the utility transh:
    transh < pdb_file > translated_pdb_file
transh is an awk script that recognizes InsightII style names and replaces them with UHBD style names. It also strips out all of the non-atom information from the file.

At this point it is advantageous to remove the many non-polar hydrogen atoms, as this action will facilitate the surface-to-surface adjustment without introducing a large error to the electrostatic energy values. The utility striph will strip the non-polar hydrogen atoms. In order to use striph, a charge file must be specified. The charge file specifies the partial charge and radius of each atom type. You may use the included .amber charge file which is extracted from the Amber list of partial charges. This file is tuned to the testing examples supplied with the alpha-release of DOT and will almost certainly require appropriate extensions/modifications for user's docking projects. The file striph.rul is assumed by striph to be present. This file specifies which hydrogen atoms from each residue type should be preserved. The syntax for striph is:
    striph pdb_file charge_file stripped_pdb_file log_file

Step 2: Generating the potential field:

The next step is to generate the still-molecule electrostatic potential field grid (.grd file) using the program UHBD (University of Houston Brownian Dynamics) from Prof. J. A. McCammon of UCSD; the program DelPhi from Prof. Barry Honig of Columbia University; or the DelPhi module of Insight II (Molecular Simulations, Inc.). In all cases the program may need some persuading to produce a grid 128 Angstroms on a side. For UHBD compile with

make DIM_MAX=129

to obtain the desired results. There is a script included with the DOT distribution that will generate a UHBD-format command file to run UHBD. In order to use the script and run UHBD, do the following:

Create the UHBD command file using the supplied utility gen_uhbd_com. After typing the command, you will be asked to supply the following information:

Enter the fixed molecule file name (*_ts, but without extention .pdb) >

Enter charge/radius file name (<Return> to accept default charges.amber) >

Enter ion strength in mM (<Return> to accept default 145.0) >

Enter ion radius in A (<Return> to accept default 1.4) >

Enter solvent radius in A (<Return> to accept default 1.8) >

UHBD can be run using the utility run_uhbd which is included in the DOT distribution.

run_uhbd

Enter fixed molecule file name (without extention .pdb) >

The potential grid and and UHBD log will be in the files:
<project_name>.grd
<project_name>.uhbd_log

If desired, convert the UHBD potential grid to DELPHI format (which DOT expects by default). This step is not really necessary, because DOT can read the potential grid files in both UHBD and DelPhi format.

grill

Enter input file name ( *.grd ) >

Enter output file name ( *.grl ) >

Step 3: Generating the ExcludedVolume Mask (.vol) File

NOTE: there are two scripts with the same name, and only one of them pays attention to the radii.

ALSO: be careful about H atoms.

The still molecule mask file (.vol) describes the solvent excluded volume of the still molecule as well as the attractive surface layer which models van der Waals contacts. This mask is computed from the atomic coordinates of the still molecule. An attractive well is placed at each atomic center. This is done by setting the mask value to -1. A smaller repulsive core is then placed at each center by setting the mask value to a positive number larger than the number of atoms in the moving molecule. The van der Waals correlation is positive if there is a collision. Otherwise it is equal to -n, where n is the number of the moving molecule atoms in the attractive layer.

In order to build the still molecule mask, use the DOT utility pdb_to_vol. This utility expects output from the striph utility described above.
pdb_to_vol pdb_file vol_file width radius
where
pdb_file	Input PDB format file
vol_file	output excluded volume file
width   	The width of the van der Waals
		attractive layer (Angstroms)
radius		The fixed radius assigned to
		all atoms (Angstroms); if
		radius = 0, then the radii will
		be assigned to atoms according
		to values in the radii table.
The pdb_to_vol utility calls pdbtoxyzr script to assign the radii according to the atom type in the .pdb file.