Vmd psfgen patch

In addition, some features of psfgen are not yet available in AutoPSF. This page provides documentation on basic use of AutoPSF.

For more detail, please read this step by step technical description of how it works and what it does. Different sections of the GUI will be enabled or disabled as you go through the procedure. Two buttons at the bottom are available at any point: Reset Autopsf which will return you to the beginning and I'm feeling lucky which will attempt to finish the PSF and PDB automatically with the information you have given so far. The stages of normal use are as follows:. AutoPSF acts on exactly one currently loaded input pdb file, specified by the Molecule pulldown menu.

The output files will have prefixes specified by Output basename. You may specify one or more topology files in the Topology files menu; a sensible default file is provided, but you will need to include others if you have nonstandard residues in your structure. The checkboxes in this section select which parts of your loaded pdb will be included in the final structure. Leaving "Everything" checked will cause the entire pdb to be included in the final structure.

Protein and Nucleic Acid components may also be selected. The "Other selections" box allows you to type in an arbitrary VMD selection text for extra atoms to include. This can be useful, for example, to include a ligand molecule but exclude crystallographic waters.

The "Chains Identified" dialogue shows a list of chains identified in your structure using the selections from the previous section. Each chain includes a length in residues , start and end atomic indices, and the N and C terminal patches to be applied. If the chain selections it has made are incorrect, you may edit, add, or delete chains from the list.

Once you have the proper chains chosen, clicking "Create chains" will parse your input files and find any non-terminal patches which AutoPSF things are needed. Patches The "Patches" menu provides an interface for adding or removing patches to be applied to your structure. A number of patches, such as disulfide bonds, may be automatically generated by AutoPSF and will be shown here. New patches may be applied, or displayed patches deleted, using the "Add patch" and "Delete patch" buttons.

Note that it is necessary to push this button to finish the PDB even if no patches are displayed. It worked!!! I tried the autopsf way first, and that appears to have made some aliases that stuck around when I tested the script. The error is: psfgen Info: generating structure Just load your pdb, then click the buttons in the appropriate order top to bottom. It guesses the waters correctly and picks up that it is meant to be DNA automatically. If you only care about this particular pdb, this is the easiest way to do it.

However, that is no fun, so here is how I'd do it manually, since to me, "manually" means writing a script for it, which makes it much more flexible if you want to do something strange in the future. These scripts to make psfs are pretty generic, and always do three things: load a topology file, create a segment, and assign atomic positions to atoms in the segment.