VMD WritePDB

VMD (Visual Molecular Dynamics) is a molecular visualization and analysis software designed for biochemistry and molecular biology. WritePDB is a command in VMD that allows the user to write out selected atoms from the molecular structure as a PDB file. This command can be very useful for analyzing trajectories from molecular dynamics simulations or for creating initial structures for new simulations.

Basics of WritePDB Command

The basic syntax for the WritePDB command is as follows:

vmd > set sel [atom selection to be written]
vmd > set outfile [output file name]
vmd > set type [file type: "pdb" or "xyz"]
vmd > writepdb $outfile $sel type $type

This command takes three inputs:

• $sel is the selection expression of atoms to be written, which can be specified using the same syntax as the "select" command.
• $outfile is the output file name, which can be any string that the user wants to name the PDB file.
• $type is the file type, which can be either "pdb" or "xyz". For this command, we will be focusing on the "pdb" file type.

Using the WritePDB Command

Here is an example of how to use the WritePDB command in VMD:

vmd > mol new myprotein.pdb
vmd > set sel [atomselect top protein and noh]
vmd > set outfile myselection.pdb
vmd > set type pdb
vmd > writepdb $outfile $sel type $type

In this example, we first load a PDB file ("myprotein.pdb") into VMD using the "mol new" command. We then select a subset of atoms within the protein that we want to output using the "atomselect" command. In this case, we only select protein atoms without hydrogens. We then set the output file name to "myselection.pdb" and the file type to "pdb". Finally, we use the "writepdb" command to output the selected atoms to a PDB file.

Conclusion

The WritePDB command in VMD is a powerful tool for selecting and outputting specific atoms from a molecular structure as a PDB file. While this tutorial covered the basic syntax and usage of this command, there are many advanced options that can be used for more complex analysis. For more information on the WritePDB command and other VMD tools, please refer to the VMD documentation or the VMD online tutorials.