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.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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Received on Wed Jul 11 2007 - 06:07:34 PDT
