by Rance Shaw to start up VMD in text mode go to directory in which your files are located. In our case it is Desktop/INL_files/IGB_restrain_backbone/newIGB_restrain/ COMMANDS: vmd -dispdev text A.prmtop annealing-prod-stride10.dcd.aligned.dcd *this starts up VMD in text mode and loads the aligned .dcd file into the trajectory file set protein [atomselect top protein] *this sets $protein to include all the atoms of the protein measure sasa 1.4 $protein *this measures the sasa of the protein not including the PEG chain and setst he probe radius to 1.4 angstroms now, to measure the sasa of the exposed hydrophobic residues set $hyd [atomselect top "protein and hydrophobic"] repeat the measure command above For SASA calculations, load the trajectory file into VMD. Go to the extensions tab, choose analysis then timeline. This will open up a new window. Go to the calculate tab and choose sec. struct. to get a graphical representation of how the secondary structure changes over the course of the simulation. |
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