From: Xin Chen (xinchen_at_ic.sunysb.edu)
Date: Thu Jul 29 2004 - 17:18:36 CDT
Dear NAMD users,
I try to use the configuration file for pair interaction at:
http://www.ks.uiuc.edu/Research/namd/current/ug/node39.html
But got a error message like this:
Info: Configuration file is pairs.namd
Warning: Couldn't parse line 60 in configuration file pairs.namd. The line
was: }
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: incr
ERROR: run
ERROR: while
ERROR: coorfile
ERROR: set
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
It seems that the NAMD can not recognize the command like "run", "set" in
the configuration file. It even cannot recognize "}". How we can make it
recognize them?
The configuration file is as follows:
# initial config
coordinates alanin.pdb
temperature 0
# output params
outputname /tmp/alanin-analyze
binaryoutput no
# integrator params
timestep 1.0
# force field params
structure alanin.psf
parameters alanin.params
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 pair.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2
# First frame saved was frame 1000.
set ts 1000
coorfile open dcd /tmp/alanin.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
Sincerely yours,
Xin Chen
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:49 CST