AMBER Archive (2007)

Subject: Re: AMBER: Could not find cntrl namelist

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Jul 09 2007 - 15:53:43 CDT

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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