VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Sep 16 2013 - 12:49:15 CDT

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:

 }
> set fitmolid [mol new $psf_file]
> mol addfile $fit_pdb_file
> set basesel [atomselect $fitmolid $fit_selection_text]
>
}

however, I am unable to connect this to the error message.

Thanks for advice

francesco pietra