Hi Tormod,
I was looking over your email and noticed that according to the partial
leap.log file you included, you are loading parm99.dat and are using
amber6. According to the amber6 release, parm99.dat does not exist.
There are parm98.dat, parm96.dat, parm94.dat, parm91X.dat, and
parm91.dat, but no parm99.dat. Are you using a modified version or did
you change the name of one of the parm*.dat files? Leap should have
complained and not written out a prmtop file. Did you check to see
where the IB ions were added in the structure (I.E. edit toto). Please
send the entire leap.log file so we can track down the problem.
Thanks,
Rhonda
On Tue, 30 Mar 2004, Skauge Tormod wrote:
> 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).
>
> thanks,
> Tormod Skauge
>
>
> Details:
>
> 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
> GApU_duplex_he_ib.rst
> 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
>
> &cntrl
> 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,
> &end
> #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
> 5.0
> RES 1 99
> END
> END
> &cntrl
> 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
> &end
>
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Received on Tue Mar 30 2004 - 19:53:01 PST
