At this step we can proceed and add counter ions to neutralize the charge. The structure has a -22 charge which is expected since we have 22 phosphate groups. WARNING: The unperturbed charge of the unit: -22.000000 is not zero. We now load our DNA structure with the command loadpdb and asign it to the variable dna: > dna = loadpdb A-dna.pdbĬheck our structure for possible errors: > check dna This will load the water model known as Optimum Point Charge ( OPC) and the ion parameters that have been shown to be compatible with that current water model. The current AMBER instruction are designed to load the water model and the ions model recommended: > source Since the molecule we are using has a negative charge, we load the ions force field so we can use them to net neutralize our system. In tleap, if we type the comand list, we can now see all the residues that we have loaded: > list Which means that we are loading the ff99bsc0 modifications for the alpha/gamma dihedrals plus the OL1 set of modifications for the epsilon/zeta dihedral and the OL4 modifications for the chi angel.
For nucleic acids, it loads: OL15 force field for DNA (99bsc0-betaOL1-eps-zetaOL1-chiOL4) see Source the force field, which has the name 15 $ source 15Īs you can see, when the force field loads, there is a line which states what modifications are being loaded. 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 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 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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