Hydrogen Bond Analysis

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To calculate RMSd we used PTRAJ from the AMBER package and then we compared the conformation of the enzyme after the simulations at the 0.1 ps interval. [7]
2.8.2. The Hydrogen Bond Analysis
Hydrogen bonds formed between residues of the protease and between residues and water molecules, were analyzed using PTRAJ. Only bonds with a distance less than 3.5 Å with the angle of interaction greater than 140 ° were considered. The output file gave us the results which hydrogen bonds were formed, with which occupancy, distance and angle. The occupancy is the ratio of the time in which the bond is formed and the total simulation time.
2.8.3. The Radial Distribution Function
The radial distribution function is a quantitative measure for the evaluation …show more content…

water molecule). We can define the density of the water molecules at a given distance from the central atom and define solvation beads.
We used PTRAJ to run the analysis for Glu21, Leu19, Asp25 and Asp29 residues of both chains. Number of water molecules is obtained by defining spheres of increasing rays centered on the atom, and counting the total encircled molecules for each sphere regarding the central atom. The calculation is repeated for 0.1 ps interval and at the end divided the number of atoms present in each sphere by the volume of the sphere and by the density of those atoms in the system.
2.8.4. The Distance Analysis
Using PTRAJ we determined distances between some atoms and how they vary with the simulation. It was carried out for the distances between oxygen atoms of the carboxyl groups of the Asp25 residue and the oxygen group of the hydroxyl group of the Nelfinavir.

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3. Results And Disscusion
3.1. Visualisation of Results
Using the VMD software it was possible to study what changes happened in terms of the HIV-1 protease and inhibitor during the processes of solvation, minimization, equilibration and production. The results showed that the addition of the solvent (water), the hydrogen atoms, the chloride ions (added to …show more content…

(a) (b)
Figure 16. Graphical representation of the temperature as the function of time for the production dynamics in 10 ps (a) and 12,09 ns (b). The temperature reached 310,15 K.
Due to smaller dimensions of the system, pressure tends to oscilate between a previously established equilibrium value. The pressure oscilated in the range of
-250 to 250 bars and in the first 20 ps of each dynamics simulation there is no data as the pressure is set to 0 bar due to software settings in the equilibration phase
(Figure 17.)

(a) (b)
Figure 17. Graphical representation of variation of pressure as a function of time for simulation of 100 ps of production (a) and 12.09 ns of production (b).

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Volume was kept constant during the equilibration step so there is no data for the first 20 ps. The number of atoms was constant during the whole simulation, the density varies inversely of volume. At the beginning of the production phase, pressure becomes constant and volume decreases during the first 40 ps. After 40 ps, volume is constant (Figure 18.).

(a) (b)
Figure 18. Graphical representation of variation of volume as a function of time for simulation

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