Protein Data Bank (PDB) file

A full description of a (pdb) file can be found in here. Herein is a snapshot of a pdb file. The first two yellow highlighted lines are not in the file but only to show the column position of each character and number. fullrmc uses pdb configuration file because it is a flexible format and rich in information. The most important inputs are highlighted below.

0        1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890

REMARK    this file is generated using 'pdbparser' package
REMARK    Boundary Conditions: 54.0  0.0  0.0  0.0  54.0  0.0  0.0  0.0  54.0 
ATOM      1 C    CO2     1     -19.317   2.636  -9.568  1.00  0.00         1C 
ATOM      2 O1   CO2     1     -20.330   3.198  -9.506  1.00  0.00         1O 
ATOM      3 O2   CO2     1     -18.304   2.075  -9.630  1.00  0.00         1O 
ATOM      1 C    CO2     2     -23.556  16.509  -9.132  1.00  0.00         1C 
ATOM      2 O1   CO2     2     -23.275  17.063 -10.112  1.00  0.00         1O 
ATOM      3 O2   CO2     2     -23.837  15.956  -8.152  1.00  0.00         1O 
ATOM      1 C    CO2     3      12.969 -23.431   3.920  1.00  0.00         1C 
ATOM      2 O1   CO2     3      12.989 -24.310   3.163  1.00  0.00         1O 
ATOM      3 O2   CO2     3      12.949 -22.552   4.676  1.00  0.00         1O 
ATOM      1 C    CO2     4      16.999 -19.836   8.272  1.00  0.00         1C 
ATOM      2 O1   CO2     4      17.957 -20.165   7.706  1.00  0.00         1O 

In order to use all the automatic capabilities of fullrmc, one should understand the different sections of the pdb and spend time defining the initial configuration. The following table explains the different useful inputs in the pdb file.

Name	Column	Colour	Type
Atom name	13 - 16	Orange	Characters
Residue name	18 - 20	Pink	Characters
Sequence number	23 - 26	Cyan	Integer
Segment identifier	73 - 76	Green	Characters
Element symbol	77 - 78	Magenta	Characters

• Boundary Conditions: The first thing to know is that the structure boundary conditions can be given as a REMARK in the beginning of the pdb file just like the highlighted in blue line. If boundary conditions REMARK is not specified, one should set the boundary conditions using Engine.set_boundary_conditions method. Otherwise Infinite boundary conditions are set automatically.

• Elements: The column “Element symbol” is very important as it is the only way fullrmc uses to identify atoms type.

• Molecules & Unitcells: In fullrmc a molecule or a unitcell is the collection of consecutive atoms sharing the same “Residue name”, “Sequence number” and “Segment identifier”. This is very important in order to be able to build automatically groups as molecules using Engine.set_groups_as_molecules or as unitcells using Engine.set_groups_as_unitcells. Otherwise, one will have no other choice than using atoms indexes to create groups.

• Atoms Name: It is recommended to give unique atom names in a single molecule because atom names can be used to define constraints. It is therefore misleading to have names duplication in the same molecule.