Automatic Rigid Body Grouping

Introduction

For large systems, grouping the rigid bodies can be tedious and painful. I intend to automate this with a pdb file as an input. Unfortunately depending on force fields, etc., the atom name conventions in pdb can be slightly different. I will include cases in as-needed basis, so please let me know (hk286) if you want certain cases to be included.

Where

The utility fortran code can be found under svn:

~/svn/SCRIPTS/AMBER/rigidbody/groupRigidBodyINC.f90

What it does

It reads a pdb file and gives you the following files:

 coordinirigid
 rbodyconfig
 atomgroups

rbodyconfig: the local rigid body groups.

atomgroups: it is a file for GROUPROTATION moves for rotations around C-C\alpha, N-C\alpha, C\alpha-C\beta, C\beta-C\gamma, C\gamma-C\delta.

The program allows you to define three regions:

1) First region: all atom, no rigid body

2) Second region: minimal rigid body grouping

3) Third region: all atoms in this region are lumped as one rigid body

Checking

You should check if you get the right groupings for each possible case. You can do this by looking at the files.

Alternatively, I have made the utility to also produce the following files:

 viewrbody.tcl - rigid body groups
 viewCACB.tcl - GROUP ROTATION along axis C\alpha-C\beta
 viewCBCG.tcl - GROUP ROTATION along axis C\beta-C\gamma
 viewCCA.tcl - GROUP ROTATION along axis C-C\alpha
 viewCGCD.tcl - GROUP ROTATION along axis C\gamma-C\delta
 viewNCA.tcl - GROUP ROTATION along axis N-C\alpha

You can open vmd and from the command line type in: source viewrbody.tcl, etc. This visualizes the groupings.

--Hk286 15:14, 28 January 2012 (UTC)