From: Jeffrey A Tibbitt (JTibbitt_at_odu.edu)
Date: Thu May 17 2007 - 17:49:35 CDT
The pdb is a general format that is used by many different programs,
including NAMD and VMD. To write your own PDB file, you need the xyz
coordinates of every atom. If you have the Atom type, residue type,
segment name, residue number, and other parameters, they can be included as
well. To place an atom in the pdb file, write the following:
ATOM x y
z
The x-coordinate goes in columns 31-38, the y-coordinate in columns 39-46,
the z-coordinate in columns 47-54. Just place that information in a text
file, and you'll have made a pdb file with 1 atom. You can also put in the
residue type, and other information. They go in other columns and they
MUST be placed within the proper columns. They call that "fixed-format"
The pdb protocal is found at
<http://www.wwpdb.org/documentation/format23/v2.3.html>
Although there is much more you can place in pdb files, here is a summary
for what you can place in the ATOM section (you don't need each item):
COLUMNS DATA TYPE FIELD DEFINITION
------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues.
31 - 38 Real(8.3) x Orthogonal coordinates for X in
Angstroms
39 - 46 Real(8.3) y Orthogonal coordinates for Y in
Angstroms
47 - 54 Real(8.3) z Orthogonal coordinates for Z in
Angstroms
55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
77 - 78 LString(2) element Element symbol, right-justified.
79 - 80 LString(2) charge Charge on the atom.
Here is an example of the first 2 residues of a protein:
ATOM 1 N MET 1 0.671 11.609 12.341 1.00 25.30
PROT
ATOM 2 HT1 MET 1 0.878 11.250 11.387 1.00 0.00
PROT
ATOM 3 HT2 MET 1 -0.343 11.496 12.541 1.00 0.00
PROT
ATOM 4 HT3 MET 1 1.224 11.074 13.041 1.00 0.00
PROT
ATOM 5 CA MET 1 1.022 13.003 12.416 1.00 23.79
PROT
ATOM 6 HA MET 1 0.431 13.526 11.679 1.00 0.00
PROT
ATOM 7 CB MET 1 0.760 13.583 13.814 1.00 27.51
PROT
ATOM 8 HB1 MET 1 -0.036 12.993 14.316 1.00 0.00
PROT
ATOM 9 HB2 MET 1 0.420 14.636 13.719 1.00 0.00
PROT
ATOM 10 CG MET 1 2.028 13.535 14.651 1.00 42.96
PROT
ATOM 11 HG1 MET 1 2.775 14.209 14.183 1.00 0.00
PROT
ATOM 12 HG2 MET 1 2.423 12.498 14.618 1.00 0.00
PROT
ATOM 13 SD MET 1 1.794 14.025 16.386 1.00 55.70
PROT
ATOM 14 CE MET 1 0.371 15.128 16.241 1.00 54.29
PROT
ATOM 15 HE1 MET 1 -0.571 14.611 16.525 1.00 0.00
PROT
ATOM 16 HE2 MET 1 0.266 15.482 15.194 1.00 0.00
PROT
ATOM 17 HE3 MET 1 0.496 16.006 16.910 1.00 0.00
PROT
ATOM 18 C MET 1 2.489 13.190 12.019 1.00 18.31
PROT
ATOM 19 O MET 1 3.385 12.295 12.146 1.00 14.68
PROT
ATOM 20 N ILE 2 2.703 14.400 11.520 1.00 11.85
PROT
ATOM 21 HN ILE 2 1.986 15.086 11.423 1.00 0.00
PROT
ATOM 22 CA ILE 2 3.993 14.757 11.101 1.00 11.73
PROT
ATOM 23 HA ILE 2 4.600 13.866 11.037 1.00 0.00
PROT
ATOM 24 CB ILE 2 3.853 15.428 9.737 1.00 21.40
PROT
ATOM 25 HB ILE 2 3.136 16.273 9.820 1.00 0.00
PROT
ATOM 26 CG2 ILE 2 5.223 15.970 9.218 1.00 15.61
PROT
ATOM 27 HG21 ILE 2 5.950 15.136 9.118 1.00 0.00
PROT
ATOM 28 HG22 ILE 2 5.632 16.713 9.935 1.00 0.00
PROT
ATOM 29 HG23 ILE 2 5.089 16.445 8.223 1.00 0.00
PROT
ATOM 30 CG1 ILE 2 3.256 14.376 8.786 1.00 18.83
PROT
ATOM 31 HG11 ILE 2 2.268 14.054 9.178 1.00 0.00
PROT
ATOM 32 HG12 ILE 2 3.933 13.496 8.750 1.00 0.00
PROT
ATOM 33 CD ILE 2 3.077 14.919 7.383 1.00 22.19
PROT
ATOM 34 HD1 ILE 2 4.067 15.068 6.902 1.00 0.00
PROT
ATOM 35 HD2 ILE 2 2.550 15.897 7.420 1.00 0.00
PROT
ATOM 36 HD3 ILE 2 2.490 14.201 6.772 1.00 0.00
PROT
ATOM 37 C ILE 2 4.611 15.689 12.108 1.00 15.48
PROT
ATOM 38 O ILE 2 3.957 16.632 12.568 1.00 13.24
PROT
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:41 CST