From: Wen Li (liw_at_wadsworth.org)
Date: Mon Feb 07 2005 - 08:40:56 CST
Dear All,
This is my first time running namd, using AMBER topology file and AMBER
restart file on a system including an RNA-protein complex, ions and a box of
water.
An error message came from running "namd2 test.conf > test_output":
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
I attach the file test.conf below, and hope you could help me, thanks!
# NAMD CONFIGURATION FILE FOR an RNA-Protein complex
#input files using AMBER topology file (parmfile myAmberParam.top)
#and Amber restart file (ambercoor myAmberRestart.rst)
PARATYPECHARMM off
amber on
parmfile myAmberParam.top #Amber topology file
readexclusions off
# this Amber restart file is for an RNA-Protein complex,
#and includes neutralizing ions and a box of water.
ambercoor myAmberRestart.rst
outputname test_nmad
#Shake to the bond H-mother atom (ntc =2, ntf = 2)
rigidBonds all
#tol = 0.0005
rigidTolerance 0.0005
#nstlim = 1000
numsteps 1000
# ntpr = 100
outputEnergies 100
ntwr = 100
restartfreq 100
DCDfreq 100
#dt = 0.002
timestep 2
temperature 30
cutoff 9
switching off
PME on
cellBasisVector1 80.1563 0.0 0.0
cellBasisVector2 0.0 78.6237 0.0
cellBasisVector3 0.0 0.0 74.9825
PMEGradSizeX 80
PMEGradSizeY 80
PMEGradSizeZ 80
Wen
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