I am trying to set up a simulation of a P450 enzyme which has a heme group with an iron atom (+3 charge) covalently bonded to four nitrogen atoms in the heme group, and to a sulfur atom in a cysteine. No matter what I've tried I always get a "valence violation" when I try to connect the iron atom to the cysteine sulfur using Maestro. How can I do this?

Use Workflows → Protein Preparation Wizard to prepare your system. It is a very easy way to set up you enzyme for modeling. Read in your file, then open the Protein Preparation Wizard and click the Preprocess button. It should prepare your heme properly, but it sets the iron charge to +2. After preprocessing, use the 'Increment formal charge' builder toolbar button to increase the Fe charge to +3.

To add the bond, use the Draw button ("pencil") on the Build toolbar. Click the Draw button, then click on the iron, then the sulfur, then click the Draw button again. Draw mode ignores valence violations, so you should not get the error message. Since the force fields do not have parameters for covalently bonded metal ions, you should change the bond to a zero-order bond with the Decrement bond order button on the Build toolbar, or right-click on the bond and choose Order → Zero.

Keywords: protein preparation

Back to Search Results