Here, I use the NAMD_2.12_Linux-x86_64-multicore package, which, after untar, it was added to PATH and renamed (so that it does not interfere with other NAMD installations), all done in Ubuntu bash:
#Vmd atomselect download
Please download them from NAMD official website, after registration. A no-CUDA NAMD 2.x version has to be called from the scripts, for the calculation. The plugin has an interface, which may be tedious to use when multiple interaction energy profiles have to be computed, thus the plugin should be called from the tcl console. VMD has a plugin named NAMDEnergy, useful when the interaction energies between sets of atoms must be computed. The resulting file can be used for further inspection or to build a line and shaded chart the file is ready for input in a python code, as presented here, bearing in mind to change the xticks and ylim accordingly. Valori = pd.concat(, join = 'outer', axis = 1) Overall, we can start VMD from where the production files are located and input in the tcl console: We can run the script over the entire protein, expecting almost no fluctuation in the previously fixed atoms (through alignment). This file also allows it to be used on an atom selection, and we choose to use only alpha carbons. Next, we need to perform the actual RMSF calculation, using the rmsf.tcl (see above) file. The ALIGN button in the RMSD Visualizer Tool and a proper atom selection would do this, but, to use it in VMD console, I provide (see above) an align_button.tcl file, which does the same procedures. However, in this case, you only want to align a specific set of atoms, namely, the ones in the transmembrane domain, provided this domain is, theoretically, fixed. The first step would be to align the protein, which you would normally do before calculating any RMSD or RMSF.
a mutation) will alter the protein behavior, by inspecting changes in the root mean square fluctuation (RMSF) for each of the atoms. You want to test whether some changes in the protein (e.g. It has an ectodomain, which is water-soluble, and one or more transmembrane helices anchoring it to the membrane. Suppose you have a transmembrane protein, and you simulate it using VMD. Aligning trajectories based on an atom selection and calculate RMSF of alpha carbons NAMD 2.x is also required for energy interaction calculations. Prior to running these commands, CHARMM-GUI for system preparation and NAMD 3.0 alpha was used for running the simulations, therefore the codes should be adapted for other production outputs. This page lists several commands and mini-tutorials useful for bioinformatics purposes in protein simulations analyses using VMD (v. align_button.tcl – a script replicating the function of the ALIGN button from the RMSD Visualizer Tool ( with regards to Bassam Haddad).
rmsf.tcl – a script for calculating RMSF over an atom selection, I got this over the internet, but could not track its original source.
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