![]() ![]() Open tleap (we do not need to use the visual interface, so tleap is the terminal version): $ tleap ![]() A comprehensive review of this force field is available in these set of published articles ( link 1 and link 2). The recommended force field for nucleic acids (DNA) has the name OL15, which is named after the city of Olomouc where it was developed in the year 2015. 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 filesÄownload 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 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. ![]()
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