From: michael atkinson (discloser2005_at_yahoo.com)
Date: Sun Sep 04 2005 - 22:21:29 CDT
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.
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 .
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)
I really appreciate your instructions if any
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