You probably need to tell us which version of sander you are using. The
name-list is version-specific. We probably should have kept those dead
entries for compatibility.
yong
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Haizhen Zhong
Sent: Monday, July 21, 2003 10:17 AM
To: amber.scripps.edu
Subject: AMBER: variable not in namelist for Sander input
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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Received on Mon Jul 21 2003 - 15:53:00 PDT
