From: Wen Li (liw_at_wadsworth.org)
Date: Mon Feb 07 2005 - 10:25:32 CST
I realized some problems in my configuration file that I attached in my
last email, and I changed them:
amber yes #not on
#PARATYPECHARMM off # this is not necessary
exclude scaled1-4 # this is required
Now I got error message:
ERROR: Margin is too small for 2 atoms during timestep 3.
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 45087 velocity is -1843.25 -441.221 -6252.94 (limit is 5000)
I was hoping that you could help on this.
---------- Forwarded message ----------
Date: Mon, 7 Feb 2005 09:40:56 -0500 (EST)
From: Wen Li <liw_at_nevis>
Subject: question on running NAMD2 using Amber files
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
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)
parmfile myAmberParam.top #Amber topology file
# this Amber restart file is for an RNA-Protein complex,
#and includes neutralizing ions and a box of water.
#Shake to the bond H-mother atom (ntc =2, ntf = 2)
#tol = 0.0005
#nstlim = 1000
# ntpr = 100
ntwr = 100
#dt = 0.002
cellBasisVector1 80.1563 0.0 0.0
cellBasisVector2 0.0 78.6237 0.0
cellBasisVector3 0.0 0.0 74.9825
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