This tutorial demonstrates how the Ante_R.E.D. 2.0 and R.E.D.-IV (June 2010) programs interfaced with R.E.D. Server can be used to (i) derive RESP or ESP charges, and to (ii) generate force field libraries for a large panel of molecules and molecular fragments. Molecules taken from the Tutorial -I- as well as new structures are presented. The goal of this tutorial is not to provide extensive explanations on charge derivation and force field library building, which can be found in Tutorial -I-, but rather to describe examples of P2N files generated and used by R.E.D. Server to build force field library(ies) with embedded RESP or ESP charges in the Tripos mol2 file format.
This tutorial might also be useful for users interested in running the R.E.D.-III.x Tools in a standalone mode (i. e. without using R.E.D. Server). However, it is important to underline that some molecular fragments and force field topology databases can only be generated using the R.E.D.-IV program. Thus, some strategies presented below might not be compatible with the R.E.D.-III.x Tools. The two logos "R.E.D.-III.x compatible" and "R.E.D.-III.x incompatible" are used throughout this tutorial to guide the reader.
It is important to underline that the Ante_R.E.D. and R.E.D. programs do not differentiate a "standard" from a "non-standard" residue. Consequently, both cases are not differentiated in this tutorial, and can be alternatively employed by the user. .
Finally, we would to suggest to R.E.D.-III.x and R.E.D. Server users to always run Ante_R.E.D. 2.0 before executing R.E.D. Indeed, errors dealing with charge equivalencing are one of the most common problem encountered when one derives RESP or ESP charge values for a new molecule or a molecular fragment. Using Ante_R.E.D. 2.0 ensures a rigorous definition of chemical equivalencing and consequently correct charge equivalencing.
|*1 Ante_R.E.D. 1.x from the R.E.D. III.x tools or Ante_R.E.D. 2.0 at R.E.D. Server||*5 Important features of a force field library:|
|*2 R.E.D. III.x from the R.E.D. III.x tools or R.E.D. IV at R.E.D. Server||- Chemically equivalent atoms bear the same charge value|
|*3 tLEaP or xLEaP (handle force fields & force field libraries):||- Two atoms belonging to a residue cannot share the same name|
|- Two atoms sharing the same name in a given residue are not recognized by LEaP !||*6 Description of the Tripos mol2 file format here and here|
|- Force field atom types are added by using a LEaP script (see an example here)||*7 Description of the mol3 file format here|
|*4 A P2N file is a PDB file with two columns of atom names:|
|Main characteristics (more information here, and an example here):|
| - 1st column of atom names reflecting chemical equivalencing|
(chemically equivalent atoms bear the same atom name; yellow column here)
| - 2nd column of atom names reflecting IUPAC naming conventions|
(two atoms belonging to a residue cannot share the same name; red column here)