Force field parameters setup

The computational details for the QM/MM simulation were almost common to those for the simulation described in Section 17.5.1. The major change was made in the setup of the real-space grids of the QM cell. The number of grid points for each axis was increased to 64 from 32 where the grid spacing h was set at h = 0.152 A. The thermodynamic condition of the MM water solvent was set at T = 300 K, p = 1.0g/cm3. The LJ parameters in AMBER95 force field were employed... 

The type of potential is chosen in the Edit/View Force Field Atom Type Parameters window of MOMEC. Note that the corresponding functions also need to be activated in the Setup/Optimization controls menu. 

In Sections 17.10-17.13 we will manipulate the force field. Make sure that you do not lose the parameters supplied with MOMEC. Therefore, copy all force field files (momec. txt) with the usual Windows98 tools (e.g., Explorer) from the directory that you use for MOMEC (e.g., c momec or c momec97 parm) to a subdirectory (e.g., c momec user lessonlO) and choose this subdirectory as the present path for the force field click on the MOMEC menu item Setup and then on Force Field. With the F2 key you can choose the path (c momec user lessonlO). Confirm with OK. 

Open the menu item Edit/View, there Force Field and there Bond Stretch Parameters. Move the cursor to the row C03-NT, click on this line, click on the button Delete, confirm and leave the Force field editor with OK. Now, your MOMEC force field does not have any parameters for Com-amine bonds you are ready to develop your own parameterization Actually, see what happens if you try to refine a molecule with a missing parameter Open the [Co(NH3)6]3+ - hin file from Section 17.1 (Setup/Files) or from the CSD and refine it (set the maximum number of cycles (Setup/Optimization Controls) to 2 Execute/Geometry Optimization). At the bottom of the Summary window the Force Field Messages will tell you that there is no bond stretch function for atom types C03 NT. 

Return to the menu item Bond Stretch Parameters under Edit/View and Force Field. Go back to the row that you have deleted, click on the Insert button and type in the top row C03, NT, 2.25, 1.950 and Section 17.10. Confirm these entries with Assign and Save the changes to the force field. You are now ready to refine the two molecules as you have learnt in Sections 17.2 and 17.4 (do not forget to set the number of cycles (Setup Optimization Controls) back to 20 refine the molecules as a Batch-Job and see the results with Batch-Job Results under Edit/ View (see Section 17.4). 

You can input the two structures from the CSD. However, it is a good exercise to build the structures using HyperChem and then refine them with MOMEC. Do not forget to set the force field back to the original MOMEC parameter set (Setup/ Force Field/c momec97 parm). For [Co(trans-diammac)]3+ it is sufficient to build one of the three conformers, refine it and then create the others by inversion of one or two of the five-membered chelate rings in HyperChem (see Section 17.3). 

Once you have created the five structures and saved the. hin files (we use the file names codmld.hin, codmdd.hin, codmdl.hin, cotrapl.hin and cotrap2.hin) you can refine them with the force field that you have developed in Section 17.10 Setup Files/Force Field/c momec user lesson 10. Check the parameters again ( b(C03-NT) = 2.25 r0(CO3-NT) = 1.927). Refine all files in the Batch Job mode. Relevant experimental data and those that you have calculated are assembled in Table 17.11.1. 

We now determine the hole sizes of the various conformers of sar. Prepare the files of the six conformers of [Co(sar)]3+ by selecting the six Co-N bonds (Tools/ Build Selections) in each file to set up the constraints for the Energy calculations. Use the. out files but rename them as. hin. As outlined above, the strain energy vs. metal-donor-distance plots for the computation of the hole sizes need to be metal ion independent. Thus, you need to activate the option Without Energy of Selected Terms in the Energy setup window. Also, the donor-metal-donor valence angle term needs to be switched off, since this is also metal ion dependent. You can do that in the Edit/View/Force Field/Atom Type Parameters menu or in the Edit/View/Parameter Array window. Both options have been used before in this tutorial. 

Note that the optimization parameters can influence the results of a molecular mechanics calculation. The activation of interaction types (in the calc-setup-momec-mm-optimizations section) that are not relevant (e.g., out-of-plane interaction) will only marginally increase the time taken for minimization, but this might lead to additional force-field messages in the log-Err window. 

The focus in development of the OPLS-UA model was on the non-bonded parameters, which historically had been the most problematic, and the new approach was to perform large numbers of Monte Carlo statistical mechanics simulations of pure liquids for their refinement. This advance was made possible by increases in computer resources and the development of flexible, efficient software, namely, the BOSS program and its predecessors, that allowed rapid setup of simulations for new systems. The key point was that a principal application of such force fields was in condensed-phase simulations including protein dynamics, and testing of the force fields on prediction of well-characterized condensed-phase properties was needed. Minimally, reproduction of liquid densities and heats of vaporization provides some confidence in both the size of the molecules and the strengths of their intermolecular interactions. Furthermore, these quantities are obtained from both experiment and simulation with high precision. 

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