This tutorial presents the execution of the Ante_R.E.D.-1.x and R.E.D. III.x programs to derive RESP charges for (i) whole molecules and (ii) molecule fragments using the dimethylalanine (AIB, 1-aminoisobutyric acid) dipeptide as example. RESP charge derivation involving $n molecules, $i conformations and $j orientations are described in a sequential approach.
Although eight different charge derivation procedures have been developed in the R.E.D. III.x program, it is important to underline that only RESP charge derivations useful in simulations based on the Cornell et al. force field (and its different adaptations) are demonstrated in this tutorial. Many examples and choices made are described, and whole data generated from R.E.D. III.x runs are available for download. However, RESP charges required for force field simulations using the GLYCAM force fields, and ESP charges used in some CHARMM, OPLS and even AMBER force field simulations can also be generated following similar strategies to those presented. Moreover, by changing few parameters in the R.E.D. source code, an infinite number of different procedures can be developed. Thus for instance, by modifying a single line in the R.E.D. III.x source code, charge values compatible with the Duan et al. force field can also be derived.
This tutorial has been tested on a laptop with a single PIV 2.4 GHz cpu and with 1 Gb RAM under Linux Fedora Core 4.0 (kernel 18.104.22.168) using the 22 NOV 2004 (R1) GAMESS version, the Gaussian 1998 RevA.11.4 version and the RESP version from AMBER8 (RESP was recompiled using qtol = 0.1d-5, maxq = 5000, maxlgr = 500 and maxmol = 200).
|*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)