Appendices

Appendix A : File Formats

The following file types are described below:

Grasp Surface File

DelPhi Potential Map

DelPhi Charge File

DelPhi Size File

PDB File (and Grasp variants)

Grasp Property File

Grasp Script File

Pair Wise Interaction File

Grasp Surface File

This unformatted file starts with five "lines" of eighty characters. The first line

contains a format specifier, i.e. the words "format=1". (There are no other

formats at this time.) The second and third lines contain key words for the

information contained within, i.e. "vertices" for the vertex positions, "accessible"

for the associated accessible surface point coordinates, "normals" for the normal

vector (of length unity) for each vertex, "triangles" for the triangle index list. The

latter is a list of integers such that entries i-2, i-1 and i, where mod(i,3)=0, give the

which vertices make up triangle i/3. NOTE that the index integers for the

triangles are INTEGER*2 ! Line three contains which variable are also written to

this file, "potentials", "curvature", "distances", "gproperty1", "gproperty2" being

the key words for the appropriate quantities. Line four contains the number of

vertices, the number of triangles, the grid size of the lattice used to create it (i.e.

the number of points along one edge of the cube, always =65), and the reciprocal

lattice spacing. Line five contains the midpoint of the coordinate system from

which the vertices were derived (i.e. the midpoint of the Grasp box). The data

then follows in the order of the keywords. Note that all are REAL*4 except for the

triangle indexes which are INTEGER*2.

DelPhi Potential Map

This is also an unformatted file. Its contents follow the format:

---

character*20 uplbl

character*10 nxtlbl, character*60 toplbl

real*4 phi(65,65,65)

character*16 botlbl

real*4 scale, mid(3)

Here phi contains the map information, mid the grid midpoint, scale the reciprocal

grid spacing. The rest are just character strings containing non-Grasp

information.

DelPhi Charge File

This file can have any number of header comment lines as long as the first

character is an exclamation point "!". After the last comment line should appear a

line as below,

atom__resnumbc_charge_

Any comments after this line must be to the right of the first twenty second

character of the line, since this part of the line is not interpreted as an

assignment.

To make an assignment statement the user places the atom name

specification under the four characters "atom" in the above line, the three

characters of the residue name under "res", the number of the residue under

"numb" and the chain designator under "c". Finally the charge value is placed

under "charge". If a descriptor field left totally blank is treated as wild, i.e. if the

chain specifier is blank the assignments spelt out by the other fields in that line

are applied to all chains in the molecule. However, blank spaces within a field

are treated as true blanks, i.e. a "c " in the atom field will not apply to a "ca "

atom. This is different from how DelPhi radii files are dealt with as is described

below.

Individual assignment statements are interpreted identically in both Grasp and

DelPhi. However the method of eventual assignment differs. In DelPhi each

such specifications are entered in a hash table. When all lines are read the

charge assigned to a particular atom is that which is most specifically declared in

the assignment statements. On the other hand the method Grasp uses to assign

charges from a DelPhi charge file is that each line is interpreted individually

before the next is read.

As an example of the different approaches, the lines:

atom__resnumbc_charge_

nz lys 25 A 0.0

nz lys 1.0

will charge all zeta nitrogens of the molecule for Grasp, and all BUT lysine 25 on

chain A in DelPhi. If the line order where reversed however the charging would

be identical since Grasp would change the charge on lysine 25 on chain A back

to zero after first setting it to 1.0. Hence when using DelPhi charge files in Grasp

be sure that the more general charge assignments precede the more specific.

DelPhi Size File

The radii assignment files in DelPhi are similar to, but simpler from, the

charge assignment files. There may again be comment lines before a "key word"

line, which in this case is,

atom__res_radius

i.e. size files only contain room for atom names and residue names.

There is one further difference between DelPhi size files and radii files,

namely that in size files empty spaces within a descriptor field are treated as wild

cards. Thus "c " under the "atom" header in a size file applies to all atoms

whose names begin with "c".

The same difference in mode of assignment between DelPhi and Grasp

occurs as is described above for charge files, i.e. the user should be careful to

put more general assignments first if the same assignment is to be made by both

programs.

Both charge and size files are supported by Grasp for a DelPhi users

convenience. However the Grasp user might want to consider using neither and

instead using the more general format of Grasp "alt" (see section on command

line syntax) commands in a script file to assign radii and charges.

Protein Data Bank File

The complete specification for these files is quite complex. Grasp (and

DelPhi) only use information on lines beginning with "ATOM" or "HETATM" or

"TER" (the latter only Grasp). These lines are expected to have format,

(A6, 5X, A5, X, A3, X, A1, A4, 4X, 3F8.3)

in the first fifty four characters, where A6 is the"ATOM " or "HETATM" header,

A5 is the atom name (only four of which are used in Grasp), A3 the residue

name, A1 the chain name, A4 the residue number and 3f8.3 the atom

coordinates in Angstroms.

In some files the field to the right of these (i.e. characters 55 to 80) are also

used to store information. In standard PDB format columns 55-60 are used for

the occupancy (F6.2), columns 61-67 for the B-value (F7.3). The Grasp variants

are as follows.

If the first two lines of the file are:

GRASP PDB FILE

FORMAT NUMBER= 1

then these two fields will be read in as the radius and charge of the atom in that

order. If the first two lines are:

GRASP PDB FILE

FORMAT NUMBER= 3

Then the values in these fields are read into general property arrays one and two

respectively. If instead they are:

GRASP PDB FILE

FORMAT NUMBER= 2

then the entire field of 55-80 is read in free format as general properties one and

two. This clearly allows the user to store values to much higher accuracy.

Note that in using any of these formats there MUST be two numbers in some

format or an error may occur.

End of molecule statements, i.e. "TER" lines should occur after each molecule

described in a PDB file for Grasp to treat them as independent molecules.

Grasp Property File

These ascii files contain a listing of a single property for either all atoms or all

surface vertices. The user may write as many comment lines as desired before a

line which has the key word "surface=" or "atoms=" (so be careful not to include

these in comment lines). All lines after that are assumed by the program to be

numerical values (in any format). On the same line as the above key words the

user should have one of the following: "potential", "distance", "curvature",

"gproperty1", "gproperty2", "accessible", or "charge", e.g.

surface=distance

will inform the program that the list of values should be placed in the distance

array for surface vertices.

Grasp Script File.

An ascii file the user can store commands in to executed together. For

instance a set of coloring commands for atoms. Any line beginning with an

exclamation mark (!) are disregarded. All other lines are sent to the command

interpreter to be acted upon.

Interaction Energy (Matrix) File.

These come in two flavors. Both should have as their first line the words,

GRASP RESIDUE INTERACTION

The next line should either be,

FORMAT= 1

or

FORMAT = 2

The first format is more complete and expects lines in the FORTRAN format,

(a3,3x,i3,10x,a3,3x,i3,10x,12g). Here the a3 is the first residue name, i3 the

residue number, a3 the next residue name, i3 the next residue number, finally

12g is format of the interaction energy.

The second format contains only the residue numbers and the interaction

strength, i.e. (i5,x,i5,4x,g12). There can be at most 10,000 lines of such

descriptions. There is no provision for comment lines. Reading in a file

automatically replaces all previous interaction values.