9/19/2023 0 Comments Vmd tutorialsGmx cluster -n selection.ndx -cutoff 0.125 -f trajectory.pdb -s first_frame.pdb -method gromos -o -g -dist -ev -sz -tr -ntr -clid -clįor information on each of these g_cluster parameters, see We need to create a file that has two atom selections, one containing the indices of all the C-alpha carbons (contained in the file alpha_carbons_indices.ndx), and one containing the indices of all the active-site C-alpha atoms (contained in the file active_site.ndx). If any index has fewer than four digits, it has to be right-justified by adding extra spaces (not tabs). Where the “XXXX” represent the indices of the atoms of that atom selection. XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX XXXX From the command line, extract just the residue index numbers like this: Fortunately, the residue indices are not changed, so let’s just save those. Unfortunately, VMD re-indexes all the atoms when you save a new pdb file, so atom indices in your new file (active_site.pdb) do not match the indices in the original PDB containing the entire protein (trajectory.pdb or first_frame.pdb). Name your file active_site.pdb.Įdit the PDB file in an editor to remove all lines but the coordinate data. Make sure you are saving only one frame (First = 0 and Last =0 ) in this window.Ĭlick on the “Save…” button to save the PDB file. In the “Selected Atoms” field, type something like: same residue as protein within 10 of resname LIG Right click on the protein name in the VMD main menu. To get the indices of the atoms of the active-site residues, save a PDB file containing only the relevant active-site residues. Same residue as protein within 10 of resname LIG While there are various methods to identify active-site residues, you can start with the first frame of your trajectory (from the NETCDF file) and use VMD to identify all protein residues within 10 Angstroms of the ligand. Thus, we must identify the residues that line the active site. Typically when clustering protein trajectories for drug design purposes, you want to know about the various conformations of the protein active site. Step 2: Identify the Protein Residues that Line the Active Site Now, your first frame is also ready for our clustering exercise. (Or you can use the command lines shown above). Edit the PDB file in an editor like vi, gedit, etc to remove the VMD-generated header.Click on the “Save…” button and save the PDB file first_frame.pdb. In the Frames section, set First and Last to 0, and Stride to 1.Right click on the trajectory name in the VMD main menu.You also will need to prepare a separate PDB file for the first frame of your trajectory. Tip: Instead of generating multi-frame PDB files of the trajectories in VMD gui, you can alternatively use a cpptraj script to get the same output. These two things could be done by any text editor, but it will be faster to do by running command lines like below in your terminal. Second, we need to replace the END delimiters used by VMD to separate frames by the ENDMDL delimiters that Gromacs uses. First, we need to delete the VMD-generated header. Now we need to edit the trajectory.pdb file to be Gromacs-compatible.Click on the “Save…” button and save the PDB file trajectory.pdb.In the “Selected Atoms” field, type protein.Now right click on the trajectory name in the VMD main menu.Or to align by all backbone atoms, replace protein with backbone. To align by all alpha carbons, for example, replace protein with name CA. Change this to whatever atom selection you wish to use to align the trajectory. In the new window that popped up, the large text box initially contains the selection protein. In VMD, click on Extensions => Analysis => RMSD Trajectory Tool. For example, one might choose to first align the trajectory by the protein alpha carbons, and then to cluster based on the positions of the residue atoms lining the active site.
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