Missing force field parameters

There are two possible routes. The first is to estimate the missing parameters by comparison to force field parameters for similar systems. If for example there are no... 

There are two possible routes. The first is to estimate the missing parameters by comparison to force field parameters for similar systems. If for example there are no torsional parameters for rotation armind a H-X-Y-O bond in your molecule, but parameters exist for H-X-Y-C. then it is probably a good approximation to use the same values. In other cases it may be less obvious what to chose. What if your system has an O-X-Y-O torsion, and parameters exist for 0-X-Y-C and C-X-Y-O, but they are very different. What to choose then One or the other, or the average After a choice has been made, the results should ideally be evaluated to determine how sensitive they are to the exact value of the guessed parameters. If for example the guessed parameters can be varied by 50% without seriously affecting the final results, the property of interest is insensitive to the guessed parameters, and can he trusted to the... 

FEP calculations reported in the literature were carried out without explicit inclusion of polarization contributions. Despitp missing polarization contributions, free enei ies calculated by means of molecular mechanics force fields generally are in good agreement with experimental results. One reason may be that molecular mechanics force field parameters are derived such that polarization contributions are included implicitly. Another reason may be that polarization errors cancel during calculations of relative free energy differences for two similar systems. 

We should check whether the structure is complete. Is the resolution of the structure adequate for our purposes Does it contain aU amino acids Are there any missing atoms Do we have force field parameters for prosthetic groups/ligands/metal ions/etc. and exotic stuff present in our favorite protein One should always check the biological unit entry in PDB to avoid misunderstanding of the real structure of a protein of interest. 

Molccti lar mcchan ics depends on the con cep I of atom types and parameters associated with these atom types. Since the number of atom types is veiy large foi the tin iverse of possible molecules, parameters will probably he missing for a random new molecule tin less a force field has been developed for molecules sim ilar lo the new molecule. Molecu lar m ech an ics predicts how the new molecule will behave based upon the behavior orknown, similar mole-cu les. 

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

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. 

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