Line 7: Coordinates of missing atoms (like hydrogens) are guessed based on residue definitions from the topology file.Old segment labels will be overridden with the new segment label ``U". Line 6: Coordinates are read from ubqp.pdb and residue and atom names are matched.The segment command also adds hydrogen atoms. Line 5: A segment called U is created, containing all atoms from ubqp.pdb.Since isoleucine contains only one carbon atom, the psf file does not use the number label after ``CD".
Line 4: The atom named ``CD1" ( carbon) in isoleucine residues is renamed as ``CD", its proper name from the topology file.See the science box below for more information. HSE is one of three names for histidine, based on the protonation state of its side group. Line 3: Change the residue name of histidine to the proper name found in the topology file.Line 2: Load the topology file top_all27_prot_lipid.inp.This line requires that the psfgen package is available to be called by VMD. Line 1: You will be running psfgen within VMD.Each command of the pgn file is explained: The file you just created contains the necessary commands to create the psf file of ubiquitin with hydrogen atoms and without water. Quit the text editor by clicking File Exit. Be sure that you are in the 1-1-build directory and enter theįile name as ubq.pgn. In a Terminal window type nedit to open the text editor.ħ After typing this, save the file by clicking File In order to create a psf, you will first make a pgn file, which will be the target of psfgen.
The psfgen package of VMD is very useful in this regard.
We will create the psf file manually to teach you exactly how it is done. Note that VMD offers an automatic psf file builder via the VMD Main menu by clicking Extensions Modeling Automatic PSF Builder. In the previous step you have created the file ubqp.pdb, which contains the coordinates of the ubiquitin alone without hydrogens, in the 1-1-build directory.Ħ Now, you will create the psf file of ubiquitin. If you are not, navigate there using the ls command to list files and directories and the cd command to change directories. Be sure you are in the 1-1-build directory. 4 Choose the Extensions Tk Console menu item and in
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