Chapter 9. ATOMS and HETATMS in the same molecule

Small molecules may be treated as ATOMS (or Extended ATOMS) if the molecule is explicitly defined in Datafile GRUB, and the small molecule mannose provides an example of this. Similarly, macro-molecules may be treated as HETATMS. Furthermore macromolecules and small molecules may be mixed together in the same PDB file, so long as all the ATOMS are listed in the file before any of the HETATMS. However discrepencies can arise if ATOMS and HETATMS are mixed together IN THE SAME MOLECULE.

A particularly important case occurs when an unusual amino-acid is needed in the middle of an otherwise normal amino-acid sequence. Sometimes, of course, the unusual residue will be found in Datafile GRUB, and then there is no problem. If the unusual residue is not in GRUB, please contact us at http://www.moldiscovery.com so that we can compute appropriate parameters. However, this computation and checking can take some time, and you may want to proceed in the short term as shown for the following example:

AA1-AA2-AA3-AA4-AA5

in which AA1 to AA5 are five consecutive amino-acids in a PDB file. In this example numbers 1, 2, 4 and 5 are ordinary residues found in Datafile GRUB while AA3 is unusual. AA1 is the N-terminal residue, and AA5 is at the carboxy terminus of this pentapeptide sequence. The ordinary residues are represented by ATOM records in the PDB file, but AA3 is HETATMS.

The first step must be to edit the file, so the HETATMS all come after the ATOMS. This is always required before input to GRIN, and gives the following layout for the PDB file:

AA1    (ATOM RECORDS)
AA2    (ATOM RECORDS)
AA4    (ATOM RECORDS)
AA5    (ATOM RECORDS)
AA3    (HETATM RECORDS)

One must use a TER card after the last ATOM record (assuming that it is the end of the sequence), and there must be an END card after the last HETATM record at the end of the PDB file. Moreover an NAMIDE card is needed before AA4 (in the present example), because a break in the sequence of ATOM records occurs at this point. This NAMIDE card ensures that the backbone amide nitrogen of AA4 is treated like a mid-chain amide, and not as a cationic N-terminal nitrogen atom. (The use of such cards is a regular feature of GRID, as described below under the Heading PROTEIN DATA BANK INPUT).

The PDB file will then be arranged like this:

AA1    (ATOM RECORDS)
AA2    (ATOM RECORDS)
NAMIDE
AA4    (ATOM RECORDSS)
AA5    (ATOM RECORDS)
TER
AA3    (HETATM RECORDS)
END

Of course each ATOM in the file must have the correct ATOM name as specified by Datafile GRUB and the conventions of the Protein Data Bank at Brookhaven, but one still needs to check the atom names of the HETATM records in amino-acid AA3. These must match the corresponding names in the HET section at the end of Datafile GRUB (See above under the Heading SMALL MOLECULE MODE), but Programme GREAT will do the checking if you use GREAT to prepare and submit your PDB file to GRIN.

Do not tell GREAT that you are "CERTAIN" that your PDB file is correct, but say you want to "MANAGE" the file. GREAT will then deal with the HETATM names, although it may be confused at each end of the HETATM sequence. This will be at the ATOM:HETATM junctions, because GREAT is only looking at the HETATMS, and so it may have to ask you some questions.

When this has been done the PDB file is ready for processing by GRIN, and will be submitted by GREAT. Then the output from GRIN can be submitted to GRID, always remembering to set Directive NETA in GRID in order to include the HETATMS as part of the Target.