![]() ![]() We can check that running a second distance command with dateset name ‘d2’ that will measure the same atoms as the ‘d1’ command. The generated trajectory: distance1-filtered.nc will only contain 271 frames, that correspond to the frames where the ligand is within 2.0-4.0 angstroms from the phosphate atom. The results are stored in the filter.dat file that marks with a 1 if the frame fall within the filter’s range and with a 0 if it does not.įor the first 10 frames of filter.dat: #Frame Filter_00003Īt this stage, the trajectory file has been sieved and we can output this new trajectory using the outtraj command. The filter command will extract the frames that fall within the desired filter. Using the filter command, we can read the output from the distance command (calling the dataset d1) and filter the frames that are within a minimim value of 2.5 and a maximum value of 4.0 angstroms. We want to extract those frame for further processing (like measuring binding energy or analyzing the conformation of the ligand) If we plot the distance1.dat, we can see that early in the simulation, the ligand spends ~270 frames withiin a distance of ~2.5-3.7 angstroms of the oxygen atoms in the phosphate of residue 25. It will generate a file called distance1.dat with this data. The distance command will have a dataset name of d1 and will read the distance between the atom name Cu1 in residue 25 (the ligand) and the phosphate atom (P) in residue 21. When using the SHAKE method, the H-H distance is restrained (as well as the. The rms fit command will remove global rotational/translational motions in the residues 2-10 and 14-23. In the commands presented below, we use VMD to select chain A of the protein. The script reads the vacuo.topo topology and the vacuo.nc trajectory data from frame 1 to the last frame with a 1 frame off-set. We can use the filter command to filter the distance between two atoms. To further analyze those conformers, we want to extract the frames that have the ligand-DNA interaction. As mentioned above, the RMSD is merely a distance measure and is most meaningful for low. We can see from the movie (1000 frames trajectory) that the ligands are forming interactions between the phosphate oxygen atoms of the backbone and the copper center of the ligand. We will first have a quick look at the peptide using VMD. ![]()
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