AMBER Archive (2003)

Subject: RE: AMBER: variable not in namelist for Sander input

From: Haizhen Zhong (zhongh_at_umich.edu)
Date: Mon Jul 21 2003 - 11:25:38 CDT

It's in AMBER6.0

On Mon, 21 Jul 2003, Yong Duan wrote:

>
> 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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Haizhen Zhong
> Sent: Monday, July 21, 2003 10:17 AM
> To: amber_at_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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