AMBER Archive (2003)

Subject: AMBER: variable not in namelist for Sander input

From: Haizhen Zhong (zhongh_at_umich.edu)
Date: Mon Jul 21 2003 - 09:16:40 CDT

Hi there, I'm setting up a .in file for running sander with PME for an
octahedral water box for a sodium-neutralized Zinc containing protein
system. The input file is as follow,
"
 &cntrl
    imin=0,
    ntx=7,
    scee=1.2,
    ntb=2,
    ntc=2,
    ntpr=50,
    dielc=1,
    irest=1,
    tempi=300.0,
    ntt=1,
    temp0=300.0,
    tautp=0.2,
    ntp=1,
    ntf=2,
    nstlim=200000,
    ntwe=50,
    ntwx=50,
    dt=.001,
    ndfmin=6,
    jfastw=0,
    cut=12.0,
    ntwr=50,
    ntwv=0,
    ntwxm=0,
    ntwem=0,
    vlimit=20,
    ibelly=0,
 &end
 &ewald
 nfft1=90,nfft2=90,nfft3=80,order=5,dsum_tol=0.00005,
 &end
END
END
"

and the error message in log file is like this,
 "namelist read: variable not in namelist
apparent state: unit 5 named VanX_0_MD300_300_all.in
last format: list io
lately reading sequential formatted external IO
Abort (core dumped)
/users/zhongh:Permission denied. "

Can anyone tell me what's wrong in the input file. I've checked it several
times and I can not find where the errors are. By the way, can anyone give
me some references on using PME for an octahedral system for
metalloprotein (like zinc-containing protein)?

Thank you very much!

Haizhen

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