AW: Problem with parameter file in Pair Interaction Calculation

From: Norman Geist (
Date: Tue Jan 10 2012 - 00:41:23 CST

How can restarting a computer fix a file? The commenting thing sounds
better, maybe theres a keyword that namd doesn’t know, maybe because the
parameter file you want to use is in an older/newer format. Possibly the
whole section is not recoqnized. But usually this shouldn’t happen I think.
You could/should try to download the file again, from the namd homepage
would be an idea.


Mit freundlichen Grüßen


Norman Geist.


Von: [] Im Auftrag
von Boyang Wang
Gesendet: Montag, 9. Januar 2012 15:27
An: M Mahjour
Betreff: Re: namd-l: Problem with parameter file in Pair Interaction


Hi Mohammad,


you can try to comment or delete the line of error, or restart your
computer, and then your file might work. You can also use a new file


Good luck,




On Mon, Jan 9, 2012 at 7:47 PM, M Mahjour <> wrote:

Dear all,

I would appreciate that if inform me to prepare a right strategy on my
I need to solve this error:


By the way, I've used this parameter file in my simulation package and I
didn't have any problem with that !

For more clarity I brought my Pair Interaction configuration file as below:

# initial config
coordinates AAA11_p.pdb
temperature 0

# output params
outputname AAA11_p-analyze
binaryoutput no

# integrator params
timestep 1.0

# force field params
structure AAA11_p.psf
parameters par_all27_prot_lipid.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
stepspercycle 20
# Atoms in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction on
pairInteractionFile AAA11_p_analyze.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2

# First frame saved was frame 1000.
set ts 1000

coorfile open dcd AAA11_p.dcd

# Read all frames until nonzero is returned.
while { ![coorfile read] } {
  # Set firstTimestep so our energy output has the correct TS.
  firstTimestep $ts
  # Compute energies and forces, but don't try to move the atoms.
  run 0
  incr ts 1000
coorfile close

Previously, thank you for your consideration.

Sincerely yours,


Boyang Wang, Ph.D.

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