Re: abf

From: Jérôme Hénin (
Date: Tue Sep 06 2005 - 08:48:25 CDT


On Monday 05 September 2005 05:21, michael atkinson wrote:
> I tried to use the abf code, released in new version of NAMD. In ug of abf,
> an example for stretching protein is mentioned.I set all required
> parameters, psf,pdb and prm file for the simulation, but when I wanted to
> use the tcl file for applying force to the protein which exists in NAMD
> workshop files(smd.tcl)

> I got error message " setting parameter tcl from
> script failed" It seems that it is not possible to use tcl file twice for
> simulation and due to use of abf_script.tcl , it is not possible to use
> another tcl file again in configurationfile.
At least, not through the TclForces command.

> my question is how I can apply
> a new tcl file in simulation (for example smd.tcl which apply force to the
> protein) and where I should mention this file' name.
In short, you can't. And to say the truth, I can't see why you would want to.
When you're doing SMD, you're not doing ABF, and vice versa.

> my another question
> is that how it is possible to get a parameter value which is defined in a
> tcl file, in another tcl file or configuration file .(for example if we
> want to have one of abf_script.tcl parameters in smd.tcl or configuration
> file)
You can access internal variables of the ABF scripts through the ABF
namespace. For instance, $::ABF::xi is the current value of the ABF reaction
coordinate. I don't know what you want to achieve by doing this, but you may
be better off modifying the ABF code directly to suit your needs.


Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 87

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