From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
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
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 http://www.edam.uhp-nancy.fr/
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