Because this is tedious to do by hand, we will let the program do it for us. Now, we should add the other hydrogen atoms to the ligand. Now, the window should look something like this:Ĭlick on the Apply-button to make the changes. I always try to have big numbers on atoms that will be mutated in an FEP, so that they will be easily distinguished from the other atoms. Change the element to a hydrogen, and number of bonds to 1.The window will now look something like this: Then go to Tools -> Structure Editing and click on Build structureĪ new window will appear, go to the second page, Modify structure. First, select the nitrogen atom by Ctrl+Click. Therefore, we will change this atom into a hydrogen. Now there is a nitrogen atom in the ligand where it should be a hydrogen. So remove them by going to Actions -> Atoms/Bonds -> delete. The selected atoms are the atoms that do not exist in our ligands. Selecting is done by Ctrl+Click and to select more than one atom, Ctrl+Alt+Click. Next, select the atoms that are marked in the picture below. This is how you control the atoms on the screen: Now, zoom in on the ligand and center it on the screen. To remove the selected atom, goto Action -> Atoms/Bond menu and click on delete This will select everything but the ligand itself. Then, go to the Select menu and click on Invert selection. The ligand will now be marked in green at the center of the screen. First select the ligand by going to the Select -> Residue menu and click on GL9 We will start by removing all atoms except the ligand. It could be a prepared pdb-file or the raw pdb-file from the Internet. Open the pdb-file of the complex in Chimera by typing Preparatory steps - remove the surroundings The two ligands that we will prepare look like this: It contains another ligand than the two we will prepare.
The complex is based on the 1FU4.pdb pdb-file. This guide will be in the form a tutorial for setting up two glycogen phosphorylase (GP) ligands. I usually use it to add hydrogen atoms and modify ligands. Nowadays, one can do a lot of other things it is for instance totally integrated with AmberTools. UCSF Chimera is a program originally written as a molecular viewer. UCSF Chimera UCSF Chimera - preparing ligands
0 kommentar(er)
