Re: [IMP-dev] automatic force field restraint setup

[Ben Webb <>]

On 7/12/10 3:31 PM, Dave Barkan wrote:
> I was wondering if there is a quick way to set up force field restraints
> on a hierarchy of atoms generated by read_pdb()? Right now I have to
> explicitly set up three or four types of restraints myself (following
> the protocol in the charm_forcefield.py example in the atom module).
> This is likely to be re-implemented often and it would be nice if IMP
> provided an easy way to do this.

Indeed - this is a common task. I have such a simplified wrapper 
available but haven't added it yet. Note that there are several steps 
because "adding a forcefield" isn't just a case of adding a restraint, 
but also requires topology, etc. to be set up properly.

> Maybe less useful to others, but potentially to me, would be if you
> could specify a region of the protein to which to add the forcefield
> restraints (instead of the whole PDB you just read in).

You can create topology for any Hierarchy - doesn't have to be the 
entire PDB, but could be a single chain, for example.

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle