AMBER Archive (2007)

Subject: RE: AMBER: Could not find cntrl namelist

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 09 2007 - 16:38:01 CDT

Hi Francesco,

If you have the command on you Unix installation can you try running:

dos2unix eqaeqb_gb_md1_12Acut.in

if the mdin file is a dos formatted text file and you try to use it on a
unix machine you'll see these types of errors. This can often happen if you
download a text file onto a windows desktop and/or create / edit on a
windows desktop and then copy it over to the unix machine. The dos2unix
command should strip all the erroneous line feeds from the end of the text
file (which cat / tail etc don't show) and then hopefully things should
work.

Note, if you open the input file with vi it should report at the very bottom
of the screen the text format - try it on your input file and see if it
reports dos format. You'll probably also see a load of purple ^M's at the
end of each line.

If that doesn't work please attach the mdin, prmtop and inpcrd files to an
email.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Francesco Pietra
> Sent: Monday, July 09, 2007 13:54
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Could not find cntrl namelist
>
> No blank line before the one starting with #, and formatting
> was exactly as in
> tutorial 1B. Now corrected by adding a comma after 300.0 (I
> find this curious
> because I was able to run that tutorial 1B).
>
> On trying to run sander, same error. Attached is the out
> file. Of course the
> mdcrd file was not generated.
>
> Any time feasible I cut and paste on posting. Sometimes
> uneasy, when, as for
> tail -f, the outcome is printed on the terminal window of
> the machine where
> amber9 is installed, while I am at a desktop scp linked to
> the computing
> machine (VMD is on this desktop).
>
> Thanks
>
> francesco pietra
>
>
>
>
> --- "M. L. Dodson" <mldodson_at_houston.rr.com> wrote:
>
> > Francesco Pietra wrote:
> > > With Amber9 I am applying the scripts of web Tutorial 1B
> (polyA-polyT) to
> > > another case. While the tutorial run OK, and the new
> case also run OK
> > up to
> > > section 4, relaxing structure before MD, the MD itself,
> with command
> > line:
> > >
> > > $AMBERHOME/exe/sander -O -i eqaeqb_gb_md1_12Acut.in -o
> > eqaeqb_gb_md1_12Acut.out
> > > -c eqaeqb_gb_init_min.rst -p eqaeqb.prmtop -r
> eqaeqb_gb_md1_12Acut.rst -x
> > > eqaeqb_gb_md1_12Acut.mdcrd
> > >
> > >
> > > did not run, tail -f telling:
> > >
> > > "Could not find cntrl namelist"
> > >
> > > File "eqaeqb_gb_md1_12Acut.in" reads:
> > >
> > > # eqaeqb MD Generalised Born, 12 angstrom cut off
> > > &cntrl
> > > imin = 0, ntb = 0,
> > > igb = 1, ntpr = 100, ntwx = 100,
> > > ntt = 3, gamma_ln = 1.0,
> > > tempi = 300.0, temp0 = 300.0
> > > nstlim = 100000, dt = 0.001,
> > > cut = 12.0
> > > /
> > > -------------
> > >
> > > A google search did not clarify the problem. As a
> newcomer to MD I
> > apologize
> > > for posting trivial questions, if this is the case.
> > > Thanks
> > >
> > > francesco pietra
> > >
> > >
> >
> > One of the most common cause of this kind of problem seems to be
> > formatting problems. Be sure there is no blank line before the
> > one starting with '#'. Also, all entries in the namelist list
> > should be separated from the rest by a comma. I notice temp0 does
> > not conform. I'm unclear about the last line: cut = 12.0, but I
> > always end the last line with a comma as well. The error message
> > seems to indicate a slightly different problem, but check these
> > items and try again. Be sure you cut and paste when sending files
> > or parts of files to the list.
> >
> > Bud Dodson
> > --
> > M. L. Dodson
> > Email: mldodson-at-houston-dot-rr-dot-com
> > Phone: eight_three_two-56_three-386_one
> >
> --------------------------------------------------------------
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>
>
>
>
>
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