AMBER: Bad atom symbol, K+ and IB in vacuum

From: Skauge Tormod <>
Date: Tue, 30 Mar 2004 14:50:42 +0200

Hi amber users,

I'm trying to run a simulation of a RNA in vacuum. As recommended in the
amber DNA tutorial, I want to include a larger and softer counterion
than Na+ and have tried K+ and IB. Running sander for the heating
process (to 300K) fails with the comment "bad atom symbol: I" or "bad
atom symbol: K". According to ions94.lib, the definitions seem to be
correct. Any help on the matter is greatly appreciated (details below).

Tormod Skauge


The counterions were added in xleap with:
> addions toto IB 0
input files generated with saveamberparm:
> saveamberparm toto GApU_duplex_ib.prmtop GApU_duplex_ib.inpcrd
The counterions are placed correctly and labelled "IB" or "K+" in the
prmtop file. Running sander (amber6):
$ sander -O -i testrun -o GApU_duplex_he_ib.out -c GApU_duplex_ib.inpcrd
-ref GApU_duplex_ib.inpcrd -p GApU_duplex_ib.prmtop -r
bad atom symbol: I

I'm using parm99 and both parm99.dat and ions94.lib are loaded in xleap
(from leap.log):
Loading parameters: /usr/local/amber6/dat/parm99.dat
Loading library: /usr/local/amber6/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber6/dat/leap/lib/ions94.lib

The "testrun" file:
test to see if IB and K+ works
    IMIN=0, NTX=1, IREST=0, NSNB=99999,
    TIMLIM=300, IG=71277, IBELLY=0,
    IGB=1, NTB=0, GBPARM=2, GBSA=0,
    DIELC=1, CUT=12.0, SCNB=2.0, SCEE=1.2,
    NSTLIM=40000, DT=0.001,
    HEAT=0.0, NTT=1, DTEMP=0.5, TAUTP=0.8,
    NTC=2, TOL=0.0005, NTF=2,
    NTPR=200, NTWX=500,
    NMROPT=1, NTR=1,
#Chauffage de 0 a 300 K
&wt TYPE='TEMP0', ISTEP1=0, ISTEP2=40000, VALUE1=0.0, VALUE2=300.0, &end
&wt TYPE='END', &end
&rst iat=0, &end
Group input for restrained atoms
RES 1 99
  imin = 0, ntb = 0,
  igb = 1, ntpr = 500, ntwx = 500,
  ntt = 1,
  tempi = 300.0, temp0 = 300.0
  nstlim = 5000, dt = 0.01,
  cut = 12.0

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Received on Tue Mar 30 2004 - 14:53:00 PST
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