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VMD SASA Calculation

posted Jul 29, 2011, 5:18 PM by Dong Xu
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/


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

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.