Hydrogen atoms and bases were added to the PDB and PSF files made with autopsf to become normal DNA.
When I ran namd in the command prompt window, nothing contained hydrogen atoms > there is no problem with the added hydrogen.
The absence of an angle parameter means that there are no constants for the equilibrium angle for the particular three atoms, and the energy equation for the angle.
Error screen when running with par_all27_na_lipid.prm file. It is stated that there is no parameter for angular vibration motion (?) for CN7, ON2, and P2.
Error screen when run with par_all36_na.prm file. There is no van der Waals parameter for OT. I decided to add a parameter to par_all36_na.prm. I added the OT van der Waals parameter.
Secondary research results reflected. Primary research data and analysis are not reflected.
The duration of the bacteriophage DNA in the same environment as the DNA simulation environment implemented in this study was measured to be 450-500 in the actual experiment of the previous study using optical tongs. This is a value higher than 100-300, which is the value of the duration of DNA obtained by randomly arranging bases with different base compositions in this study. This shows that the DNA duration obtained in the actual experiment is smaller than the DNA duration obtained in the molecular dynamics simulation. However, it is consistent with the fact that the duration of DNA is smaller than the helix whose duration is 1000, so it is more flexible.
According to the study results according to the base composition, it can be seen that if the ratio of A-T bonds is higher than that of G-C bonds, it is more bent in a general DNA structure, and it is difficult to bend in a stable state. The property of being hard to bend is the same as the expectation that the less the number of hydrogen bonds between the two strands of DNA, the easier it will be bent. It can be considered that when the binding factor approaches the TATA box, the TATA box must have high elasticity to overcome the repulsive force with the binding factor and bind.
According to the study results according to the base composition, it can be seen that the higher the ratio of A-T bonds, the more curved and twisted in the general DNA structure. Based on the textbook content explaining that the TATA box is relatively well unwound during transcription or replication by the number of hydrogen bonds, and in addition to the results of this study, it seems possible that the more A-T bonds, the lower the elastic modulus of DNA.
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