From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Thu Feb 02 2017 - 20:46:29 CST
I remember having a similar issue with the namdenergy extension. A work
around I came up with executed the namd binary with a input file I wrote
and appended the output to a file I could extract energy values from
later. Something like:
$proteinsel writepdb $coor_filename
#writes updated coordinates
exec <dir to you binary>/namd2 insnamd.conf >> insnamd.out
#runs namd with my input file and the coordinate file written above
I think the temporary input file did not write the psf file name
correctly which caused the same error you have.
On 02/02/2017 08:44 PM, Darya Fadavi wrote:
> I tried moving the psf and dcd files to a shorter path length location
> but I'm still getting the namd2.exe stopped working error with the
> Fatal Error being it can't open the psf file.
> On Wed, Feb 1, 2017 at 12:45 PM, Goedde, Chris <CGOEDDE_at_depaul.edu
> <mailto:CGOEDDE_at_depaul.edu>> wrote:
> On Feb 1, 2017, at 12:31 PM, Darya Fadavi
> <daryafadavi_at_berkeley.edu <mailto:daryafadavi_at_berkeley.edu>> wrote:
> > Hello,
> > I'm trying to calculate energy plots (VDW, Elec, Nonbond) using
> the NAMD Energy extension. I've specified the parameter file I
> used but when I try to run it, I get the error that "namd2.exe has
> stopped working". I'm working on Windows, and I downloaded and
> extracted the entire zip file for namd, so I don't think I'm
> missing any files.
> > I then looked to the temp log file created in the current
> directory to see what the fatal error was and it says "FATAL
> ERROR: UNABLE TO OPEN .psf FILE C:UsersDarya
> FadaviDocumentsMofrad_Lab mdSUN projectMouseSun1 dxt templateWith
> KRun1mousesun1_ionized.psf". I'm not sure why it wasn't able to
> open the psf file. I've loaded it in vmd and opened the dcd file
> on top of it at stride 10.
> I had trouble with the unix version of namd choking on path names
> that were longer than about 135 characters. This might be a
> similar issue. You could try renaming or moving the file so the
> path length is shorter and seeing if that fixes things.
> Chris Goedde
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