- 1.7
- 1.6
- 1.5
- Beta
- Examples (for 1.6a)
- Misc
Once a complex NETA definition has been made for a given atom type, it is often useful to be able to reference this type in order to save repeating the same description for a closely-bound atom. The ampersand symbol allows you to do this, and specifies an integer type id to match rather than an element. As an example, consider the following definitions for trifluoroethanol from the OPLS-AA forcefield where the environment for each atom is described in full for each type:
160 CT C "-H,-H,-O(-H),-C(-F(n=3))" "CH2 in trifluoroethanol" 161 CT C "-F(n=3),-C(nh=2,-O(-H))" "CF3 in trifluoroethanol" 162 OH O "-H,-C(nh=2,-C(-F(n=3)))" "OH in trifluoroethanol" 163 HO H "-O(-C(nh=2,-C(-F(n=3))))" "HO in trifluoroethanol" 164 F F "-C(-F(n=3),-C(nh=2,-O(-H)))" "F in trifluoroethanol" 165 HC H "-C(nh=2,-O(-H),-C(-F(n=3)))" "H in trifluoroethanol"
For each atom type, the whole of the trifluoroethanol molecule is described, but each type tends to share a common chunk of NETA definitions with the other types. As an alternative, then, we can define one or two of the involved types explicitly as above, and then specify the rest of the types relative to this one:
160 CT C "-H,-H,-O(-H),-C(-F(n=3))" "CH2 in trifluoroethanol" 161 CT C "-&160" "CF3 in trifluoroethanol" 162 OH O "-&160" "OH in trifluoroethanol" 163 HO H "-O(-&160)" "HO in trifluoroethanol" 164 F F "-C(-&160)" "F in trifluoroethanol" 165 HC H "-&160" "H in trifluoroethanol"
Much neater! Or should that be 'not much NETA'? Hmmm. Anyway, reusing types in this way is a powerful way to reduce the complexity of type descriptions required for a given molecule or fragment. Typically it is advisable to pick an atom that is fairly central to the molecule and bears a lot of connections, and provide an unambiguous type description.

