CHARMM performance

Amides, alkaline hydrolysis, 215 Anharmonic systems, direct evaluation of quantum time-correlation functions, 93 Apollo DSP—160, CHARMM performance, 129/ simulations, solvent effects, 83... 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

Of the biomolecular force fields, AMBER [21] is considered to be transferable, whereas academic CHARMM [20] is not transferable. Considering the simplistic form of the potential energy functions used in these force fields, the extent of transferability should be considered to be minimal, as has been shown recently [52]. As stated above, the user should perform suitable tests on any novel compounds to ensure that the force field is treating the systems of interest with sufficient accuracy. 

Calculations performed using MC BOSS [66] with the CHARMM combination rules. Partial atomic charges (C = —0.27 and H = 0.09) were identical for all three simulations. 

The chemical reaction catalyzed by triosephosphate isomerase (TIM) was the first application of the QM-MM method in CHARMM to the smdy of enzyme catalysis [26]. The study calculated an energy pathway for the reaction in the enzyme and decomposed the energetics into specific contributions from each of the residues of the enzyme. TIM catalyzes the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP) as part of the glycolytic pathway. Extensive experimental studies have been performed on TIM, and it has been proposed that Glu-165 acts as a base for deprotonation of DHAP and that His-95 acts as an acid to protonate the carbonyl oxygen of DHAP, forming an enediolate (see Fig. 3) [58]. 

Performance. The total time for 500 steps of dynamics and 25 nonbond updates for the standard CHARMM benchmark (Brunger, A. T., Harvard University, personal communication, 1985.), a B-DNA eleven-mer duplex with 706 atoms and a 11.5 angstrom nonbond cutoff (77000 nonbond pairs) is found in Table II. 

Classical simulations of MbCO using the CHARMM force field were performed for different tautomerization states of the distal histidine residue (His64) [33], These simulations showed that when His64 is protonated at N,5 (denoted the tautomer) it often rotates such that it exposes either the N,>—H bond or the un-protonated N atom to the CO, as depicted in Scheme 3.4. We... 

We thank J. Apostolakis and Professor A. Pluckthun for helpful discussions. The calculations were performed on an SGI Indigo2 and an eight-processor SGI Challenge (R4400 processors). The CHARMM program within the version 4.0 of the QUANTA software package (Biosym-MSI Inc) was used for some of the minimization performed in this work. The CCLD program is available from A. Caflisch. 

For the construction of molecular structures, a 2D formula editor is provided in combination with 3D conversion. Standard potential energy minimization is performed using the modified parameter set of the CHARMm force field [68] the conformational models are built using Monte Carlo conformational analysis together with poling as described in the next section. 

MD simulations provide a detailed insight in the behavior of molecular systems in both space and time, with ranges of up to nanometers and nanoseconds attainable for a system of the size of a CYP enzyme in solution. However, MD simulations are based on empirical molecular mechanics (MM) force field descriptions of interactions in the system, and therefore depend directly on the quality of the force field parameters (92). Commonly used MD programs for CYPs are AMBER (93), CHARMM (94), GROMOS (95), and GROMACS (96), and results seem to be comparable between methods (also listed in Table 2). For validation, direct comparisons between measured parameters and parameters calculated from MD simulations are possible, e.g., for fluorescence (97) and NMR (cross-relaxation) (98,99). In many applications where previously only energy minimization would be applied, it is now common to perform one or several MD simulations, as Ludemann et al. and Winn et al. (100-102) performed in studies of substrate entrance and product exit. 

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