VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 17 2013 - 00:03:53 CDT

Hi,
  Just to track down what's going on here, where did you obtain the
show_replicas.vmd script you're working with? Is it from the NAMD guide?:
  http://www.ks.uiuc.edu/Research/namd/2.9/ug/node66.html
Did you try running the exact example described there, or is your problem
occuring when running your own replica exchange simulations.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 16, 2013 at 07:49:15PM +0200, Francesco Pietra wrote:
> h
> Hello:
>
> I was trying to load namd2.9 replicas into vmd with
>
> source the replica exchange conf file
>
> show_replicas.vmd
>
> whereby the starting structure nvt-02.pdb was read and then the dcd for
> job0:
>
> ..................
> ..................
> Info) Finished with coordinate file nvt-02.pdb.
> dcdplugin) detected standard 32-bit DCD file of opposite endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> Info) Using plugin dcd for coordinates from file
> output/0/fold_P2i.job0.0.dcd
> Info) Finished with coordinate file output/0/fold_P2i.job0.0.dcd.
>
> The final folded structure was also loaded, then, in the tk console
> appeared
>
> can't read "basesel"
>
> at a point that the other six jobs had be taken into consideration.
>
> I notice from the code:
>
> A }
> A A set fitmolid [mol new $psf_file]
> A A mol addfile $fit_pdb_file
> A A set basesel [atomselect $fitmolid $fit_selection_text]
>
> }
>
> however, I am unable to connect this to the error message.
>
> Thanks for advice
>
> francesco pietra 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/