Appendix A. Aliasing
I must admit right now that I am not sure I understand when aliasing is called for. The idea, I think, is to fix any non-standard notation for the amino acids and atoms that might be used in the pdb file. Aliases take the form:
alias atom residue pdbname topname
alias residue pdbname topname
The "atom" or "residue" indicates whether we are fixing the name of an atom or a whole amino acid. When an atom is being fixed, the residue it is in must be indicated by its three-letter code. Then list the name as in the pdb file, followed by the name as in the topology file.
1. As far as I can tell, the only time we need to alias a residue is for histidine, depending on whether it is neutral or protonated, and if neutral, which tautomer. The three possibilities are shown below:
2. The Table following indicates the atom names that the topology file uses. You need to inspect your pdb file, and alias any that do not match.
| Amino Acid | Three-letter Code | Atom Designations |
|---|---|---|
| Alanine | ALA | N, CA, CB, C, O |
| Arginine | ARG | N, CA, CB, CG, CD, NE, CZ, NH1, NH2, C, O |
| Asparagine | ASN | N, CA, CB, CG, OD1, ND2, C, O |
| Aspartic Acid | ASP | N, CA, CB, CG, OD1, OD2, C, O |
| Cysteine | CYS | N, CA, CB, SG, C, O |
| Glutamine | GLN | N, CA, CB, CG, CD, OE1, NE2, C, O |
| Glutamic Acid | GLU | N, CA, CB, CG, CD, OE1, OE2, C, O |
| Glycine | GLY | N, CA, C, O |
| Histidine | HIS=HSD | N, CA, ND1, CG, CB, NE2, CD2, CE1, C, O |
| Histidine | HIS=HSE | N, CA, NE2, CD2, ND1, CG, CE1, CB, C, O |
| Histidine | HIS=HSP | N, CA, ND1, NE2, CE1, CD2, CG, CB, C, O |
| Isoleucine | ILE | N, CA, CB, CG2, CG1, CD, C, O |
| Leucine | LEU | N, CA, CB, CG, CD1, CD2, C, O |
| Lysine | LYS | N, CA, CB, CG, CD, CE, NZ, C, O |
| Methionine | MET | N, CA, CB, CG, SD, CE, C, O |
| Phenylalanine | PHE | N, CA, CB, CG, CD1, CD2, CE1, CE2, CZ, C, O |
| Proline | PRO | N, CA, CD, CB, CG, C, O |
| Serine | SER | N, CA, CB, OG, C, O |
| Threonine | THR | N, CA, CB, OG1, CG2, C, O |
| Tryptophan | TRP | N, CA, CB, CG, CD2, CD1, NE1, CE2, CE3, CZ2, CZ3, CH2, C, O |
| Tyrosine | TYR | N, CA, CB, CG, CD1, CD2, CE1, CE2, CZ, OH, C, O |
| Valine | VAL | N, CA, CB, CG1, CG2, C, O |
| Amino acid structures may be found here. | ||
In the several pdb files I have inspected, the only atom that seemed consistently to require aliasing is the atom CD1 in isoleucine, which must be aliased to CD. The two atoms of leucine aliased in the script above are the two methyl groups of the leucine side chain; I don't see any point in swapping them.