We do that using the LEaP module of AmberTools. Next we need to generate the topology and the coordinate files for the system so we can run our simulation. Open the file using VMD so you can see the structure that we are going to use for our tutorial. The structure has the sequence d(CGCGAATTCGCG), which is known as the Drew-Dickerson dodecamer, or DDD, and is one of the most famous and studied short oligomers available. Generating the initial topology and coordinate filesĭownload the initial PDB structure file (A-dna.pdb) available here.

The starting structure is a type A-DNA generated using the Nucleic Acids Builder tool available as part of the AmberTools collection of programs. After the simulation we will use CPPTRAJ to analyze the characteristics of the conformational switch during the simulation. In this tutorial, we will run a DNA molecule with 12 base pairs starting in the A-DNA configuration and study the conversion to the B-DNA form. This is because the two strands are also antiparallel (they run in opposite directions), as mentioned in the previous slide.This example consists of a full set of instructions that will guide the user on how to run a simulation using AMBER and performing the analysis with CPPTRAJ. Once you figure out the direction in which one strand is read, you automatically know the direction in which to read the other strand. This slide shows how the carbons in the sugars are numbered, to help you determine which ends is 5', and which is 3'. The 5' and 3' designations refer to the number of carbon atom in a deoxyribose sugar molecule to which a phosphate group bonds. One end is referred to as 5' (five prime) and the other end is referred to as 3' (three prime). More: DNA is 'read' in a specific direction, just like letters and words in the English language are read from left to right. Sources: image from the National Human Genome Research Institute (NHGRI) Genetic Illustrations ĭefinition from the National Human Genome Research Institute (NHGRI) Thymine, and guanine always pairs with cytosine. In base pairing, adenine always pairs with Stand for the chemicals adenine, thymine, guanine, and cytosine, In DNA, the code letters are A, T, G, and C, which The bases are the 'letters' that spell out the Of sugar, a molecule of phosphoric acid, and a moleculeĬalled a base.

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