Define Unique Coarse-Grained Particle Bonds Dialog Box

Uniquely label bonds between coarse-grained particles that differ in the way they are connected, such as C-N vs N-C bonds between two amino acids.

This dialog box opens when you click the Run button in the Map Atoms to Particles Panel and there are different kinds of bonds between any given pair of particle types.

  • Features
  • Additional Resources

Define Unique Coarse-Grained Particle Bonds Dialog Box Features

Bond table

This table lists all the bonds between pairs of particles for which there is a difference in the way each pair is bonded: for example, in an alternating series ABAB... the A-B bond might be different chemically from the B-A bond. The table allows you to make the labels for the different bond types unique by adding some text to the bond label, which is then used in the force-field assignment. The columns are described below.

Bond Label Label of the bond, used in the force-field assignment. The label is updated with the particle information if you check the box in the Unique column.
View View the bond in the Workspace. The atoms of the particles for one occurrence of the bond are marked and the view zooms in so you can see the particles and the bond.
# Occurrences Number of occurrences of the bond for the particular bonding pattern represented by the table row.
Unique Make the bond labels unique by adding particle label information set in the Particle N Label columns.
Particle 1 Label
Particle 2 Label		 Set the labels for the particles that will be used to make the bond label unique. The label should uniquely identify the bonding environment. The default label includes the element symbol and other information such as a numerical index for the chemical environment and information about chirality.
Save Save the unique labels to the materials science templates in your Schrödinger user resources directory. These labels are read in when you do particle assignments later on. If you don't click this button, the labels are just used for the current job.
Reset button

Reset the data in the table to the default, discarding all changes made.

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