Live backgrounds zmatrix11/7/2023 ![]() UFF, Mopac and DFTB are identical to these methods within AMSinput, SimpleMM is a very primitive force field like method that used to be the only available pre-optimizer. If you right-click the cog wheel you will get a pop-up menu that allows you to specify which method to use as a pre-optimizer: UFF, Mopac, DFTB or SimpleMM. If you click it your system will be optimized using the UFF method. On the right end of the molecule editor tools you will see a cog wheel. Pre-optimization ¶Īfter drawing a molecule you will typically run a pre-optimization. Right click on one of the fields to propagate that value to all selected atoms (for example to change the color of all selected atoms). You can also see and change other atom properties like the type, screen radius, nuclear charge, mass, color, Amber and Tripos atom types and more. Note that only selected atoms will be visible in the Atom Details panel. It will activate the Atom Details panel, in which you an change the number of connectors and lone pairs for each atom. You can view and change these via the Atoms → Details (Color, Radius, Mass…) menu command. So if you plan to use this command it is essential that the number of connectors and the number of lone pairs is correct. The number of connectors will determine the geometry (2 linear, 3 flat, 4 tetrahedral). When you use the Add Hydrogen menu command, all unsaturated connectors will be saturated with hydrogen atoms. Some of the ‘connectors’ may be used by lone pairs and not be available for bonding to other atoms.įor example, carbon has 4 connectors and no lone pairs, oxygen has 4 connectors and 2 lone pairs. The number of connections depends on the atom type. Atom Details: Connectors (valency) and Lone Pairs, Atom mass ¶Įach atom you make has the possibility to connect to other atoms. This will switch to the select tool, and as a result you are no longer in bonding mode. To stop bonding mode, click once on the bond atom. If you next click to create a new atom, it will automatically be bonded to the bond atom. This is indicated by a line from the bond atom to the mouse cursor. When you still have an atom tool and one atom is selected, you are in bonding mode. Bonding mode ¶Īfter creating an atom, it will be selected (the ‘bond atom’). Here we will just note some details that may not be obvious. Please check the tutorials for extensive description of this. Building molecules with AMSinput is very simple, just draw them with the appropriate tools. ![]()
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