From: Darya Fadavi (daryafadavi_at_berkeley.edu)
Date: Wed Feb 01 2017 - 12:31:15 CST
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 also tried to run the energy plots in tk console using this script but I
get the same error as using the gui:
set mol1 [atomselect 0 "segname P1"]
set mol2 [atomselect 0 "segname P2"]
namdenergy -ofile 4dxt_mousesun1_1_P1P2 -exe C:/Program\ Files\
(x86)/University\ of\ Illinois/NAMD_2.12_Win64-multicore/namd2 -sel $mol1
$mol2 -vdw -elec -nonb
Is there something I'm doing incorrectly or missing?
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