RESP charges

One notes that the results of QM MM MM depend sensitively on the choice of the charges used in the Amber calculation. The use of the Mulliken charges, for instance, in QM MM MM increases the error from —47 kcal/mol with RESP charges to -86 kcal/mol. This implies that the results will also depend sensitively on how to arbitrarily scale the near-border charges for the QM-MM interaction, because the problematic QM-MM boundary is very close to the reaction center. 

Cornell, W. D. Cieplak, P. Bayly, C. I. Kollman, P. A., Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation, J. Am. Chem. Soc. 1993,115, 9620-9631. 

If separate D-RESP charge sets are fitted for every single one of the 36 frames, the standard deviation of the electrostatic field generated varies between 3.5 and 5% with respect to the full quantum reference. This accuracy is the best (in the least-squares sense) that can be obtained if the system is modeled with time-dependent atomic point-charges and represents the accuracy limit for a fluctuating point charge model of the dipeptide. 

All-atom FF for proteins, nucleic acids, organics using RESP charges Cornell 1995... 

The second term in Equation 1, . involves carrying out a Poisson-Boltzmann calculation and evaluating the exposed surface area of all atoms for all the snapshots for C, M, and L. Currently, we use Hartree-Fock (HF)/6-31G restrained electrostatic potential (RESP) charges and PARSE radii for the PB calculation within DELPHI and the program... 

Studies of the isolated imidazolium cation have been undertaken primarily to produce parameters for use in force field methods. Shah et al., have calculated the [BMIM]+ cation at the HF/6-31G(d) level, and determined CHdpG [57] charges [58]. De Andrade et al., have calculated the [EMIM]+ and [BMIM] cations at the HF/6-31G(d) level, and determined the RESP charges using AMBER [59]. They also compared the ab initio dipole moments and vibrational frequencies with those obtained using force field methods [60]. 

The electrostatic potential of the optimized molecules was generated with HF/6-31G as recommended by the developers of AMBER95 [20] and used further on for obtaining the RESP charges. The latter were generated by multi-conformational fitting [20]. All calculations were done both in vacuum and water. 

The RESP charges which were implemented in the force field are provided in Table S7. 

Analysis of the obtained RESP charges shows that the charge set generated for the dimer should be used for simulation of longer oligomers. Moreover, the values generated in vacuum would be more adequate for implementation in AMBER, since the additional effects of polarization/depolarization should be accounted for by means of direct interactions with the explicit solvent molecules the charges of which are also based on gas phase calculations... 

Supplementary Information Available online are PBE and MP2 energy data (Table SI) MP2 torsion angles with conformer population in vacuum (Table S2) and in water (Table S3) for the monomers and analogous data for the dimer (Tables S4, S5) the PBE entries of Table 26.5 (Table S6) RESP charges (Table S7) MD trajectories of control parameters (Fig. SI) rotational barrier about 02 of the dimer in water (Fig. S2). 

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