AMBER Archive (2007)

Subject: Re: AMBER: Could not find cntrl namelist

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Jul 09 2007 - 16:22:30 CDT

I believe I had tried most combinations before posting, ie, removing "#",
removing the whole line beginning with "#". Same error.

Notice that all previous scripts in the tutorial had that formatting (first
line of description beginning with "#") and they run OK on my machine.

I suspect I am doing a mistake that remains cryptic.

francesco

--- "M. L. Dodson" <mldodson_at_houston.rr.com> wrote:

> Francesco Pietra wrote:
> > 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
> >
>
> Well, that's a bummer. This is really reaching, but try removing
> the '#' from the first line. I haven't looked at the source, but
> sander might be using the # to indicate a comment, so that it
> completely ignores the # line and treats the
> &cntrl
> as the first line. Maybe one of the developers can comment.
>
> As for cutting and pasting from another machine ssh session, I do
> it all the time with no problem, but I generally just highlight
> and use the middle mouse button to paste the highlighted text. I
> use a 3-button mouse specifically because I'm so used to this
> behavior. (Yes, I know about the "chorded" middle button before
> someone chimes in.)
>
> Bud Dodson
>
> >
> >
> >
> > --- "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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>
> --
> M. L. Dodson
> Email: mldodson-at-houston-dot-rr-dot-com
> Phone: eight_three_two-56_three-386_one
> -----------------------------------------------------------------------
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