From: Rajan Vatassery (rajan_at_umn.edu)
Date: Fri Jul 15 2011 - 16:43:04 CDT
Dear Jorgen,
I believe your problem lies in the fact that you are trying to change
parameters between "run" commands. As this page outlines:
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node10.html
there are only a few parameters that can be changed between "run"
commands. On a side note, I find that page to be very useful and concise
-- definitely recommended reading before running any NAMD simulation.
The effect of this is that you are unable to write a nice, clean conf
file as you have done, and instead you simply must split the file up
into several conf files.
Hope this helps.
rajan
On Fri, 2011-07-15 at 22:55 +0200, Jorgen Simonsen wrote:
> Hi all
>
> I am trying to make a configuration file that the first run an
> equilibration with my protein fixed and from that the backbone fixed
> so I have inserted the following syntax
>
> ######################################
> if {1} {
>
> fixedAtoms on
> fixedAtomsFile protein.fix
> fixedAtomsCol B
> fixedAtomsForces on
>
> }
>
>
> minimize 10000
> reinitvels $temperature
>
> run 100000
>
> if {1} {
>
> fixedAtoms on
> fixedAtomsFile backbone.fix
> fixedAtomsCol B
> fixedAtomsForces on
>
> }
>
> minimize 10000
> reinitvels $temperature
>
> run 100000
>
> fixedAtoms off
> fixedAtomsForces off
>
> minimize 10000
> reinitvels $temperature
>
> run 500000
>
> but I get this error
> TCL: Setting parameter fixedAtomsFile to backbone.fix
> FATAL ERROR: Setting parameter fixedAtomsFile from script failed!
>
> FATAL ERROR: Setting parameter fixedAtomsFile from script failed!
>
> FATAL ERROR: Setting parameter fixedAtomsFile from script failed!
>
> the file backbone.fix looks fine - how to fix this thanks in advance
>
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