From: Peter Freddolino (
Date: Sun Jun 20 2010 - 19:09:47 CDT

Hi Neelanjana,

The procedure that you're describing is handled automatically if you use
the -updatesel flag. Apparently this flag wasn't documented yet, a
situation that I have remedied.

As Axel noted, the behavior that you're describing most likely indicates
a permission or disk space/quota problem -- you should make sure that
the files directory exists and has sufficient space available, and is


On 06/20/2010 07:27 AM, Neelanjana Sengupta wrote:
> Dear VMD experts,
> I am using NAMDenergy (in the text mode) for evaluating the
> interaction energy between 2 selections, one of which actually changes
> at each frame. Hence, I wrote out a data file containing the second
> selection at each time step. I then load the trajectory step by step,
> and evaluate with namdenergy. My code has the foll. key parts in a loop:
> mol new sys.psf
> mol addfile sys.dcd first $n last $n waitfor all
> namdenergy -sel $sel1 $sel3 -par ../par_all22_prot.inp -nonb -extsys
> sys.xsc -ofile files/en_frm$n
> Curiously, while this /worked well/ for 2 of my dcd files, for another
> dcd file corresponding to a latter part of the timeline for the same
> simulation, this does not work!! I am getting the foll. error message:
> *Info) Opened coordinate file namd-temp.pdb for writing.
> ERROR) write_timestep returned nonzero
> Info) Finished with coordinate file namd-temp.pdb.
> atomsel: writepdb failed.*
> However, the namd-temp.pdb is written out.
> Can someone help me zero in on the problem here?
> Thanks in advance,
> Neelanjana Sengupta