Adk44: Created page with "== 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 f..."

2019-05-13T11:15:33Z

Created page with "== 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 f..."

New page

== 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.

--[[User:Hk286|Hk286]] 15:14, 28 January 2012 (UTC)

Automatic Rigid Body Grouping - Revision history

Adk44: Created page with "== 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 f..."