Robert:
Thanks. I had underestimated the problem of DOS formatting just because I have
no Windows. I was already advised to type din directly on my machine; sorry for
not having appreciated that suggestion. I relied on the power of dos2unix
command, and vim did not show any strange character.
I took the mdin file for MD from tutorial 1B (Simulating a small fragment of
DNA) and did some editing with either vim or nano, don't remember which one. I
am used to prepare most things on a desktop with debian linux i386 and gnome,
then I send scp the files to the machine with debian linux amd64, where Amber9
is installed. The mdin for preliminary minimization (the one I sent with my
previous email and that was correct) had the same source. My guess is that such
DOS formatting is in the mdin for MD of the said tutorial, but I can be wrong.
As soon as I find the time, I'll repeat the process and I'll report.
Now the "cntrl namelist" issue is over, though I encountered another problem in
trying to run MD on methylcyclohexane. The error message is from fortran
runtime and I do not understand what RTM is looking for. Should it be a problem
of my installation of fortran, please do nothing more than advising me. It
would be my problem, I have already given problems enough to Amber. I must add
that the fortran runtime library provides - on that machine - correct support
to the NWChem suite (compiled with intel compilers). That was installed long
before Amber.
By ending the command line with "2> errors", I have reproduced the errors that
appear on the screen below the command line for MD. Unfortunately, I don't know
how to send the command line to a file, so that I (accurately) digit it here:
$AMBERHOME/exe/sander -O -i vac_md1_12Acut.in -o eqmecycl_vac_md1_12Acut.out -c
eqmecycl_vac_min.rst -p eqmecycl.prmtop -r eqmecycl_vac_md1_12Acut.rst -x
eqmecycl_vac_md1_12Acut.mdrd 2> errors
Attached are the relevant files.
Thanks
francesco pietra
--- Robert Duke <rduke.email.unc.edu> wrote:
> Francesco -
> Okay, this is purely a matter of nonprinting characters in the mdin file for
> the MD RUN. Unfortunately, Ross and I were misled by the mdin,
> "vac_min.in", which was for the minimization, and which was the only mdin
> sent in the group of files to the list. SO I looked at the output of
> eqmecycl_vac_md1_12Acut.out. This is the output that produces the "Could
> not find cntrl namelist" message. If you look at the echo of the mdin
> input, it looks fine here, and it is also clear we were looking at the wrong
> mdin. However, if you do an "od -c eqmecycl_vac_md1_12Acut.out > od.dmp"
> and look at od.dmp, you will see, with a little work, that there are two
> nonprinting characters, octal 302 followed by octal 240, in front of every
> mdin input line. Perhaps the mdin file was made on another operating
> system, with a different native language, or some such? You need to use an
> editor like vi on a compatible unix system, or edit the current one, getting
> rid of the apparent blanks, which I would guess are some sort of unicode and
> replacing them with true blanks. Then run the mdin you created through
> od -c again, confirming that all the nonprinting characters that previously
> showed up as octal numbers have disappeared. Most likely, this is all that
> is going on. For my edification, I would be interested to know how you
> generated this file; I have had trouble myself moving files from windows to
> linux, but I think that was a matter of /r/n instead of /n at the end of the
> lines (windows has a different line termination convention than unix). Have
> fun with the dogs; if you fix the mdin, you really should be running.
> Best Regards - Bob
> ----- Original Message -----
> From: "Francesco Pietra" <chiendarret.yahoo.com>
> To: <amber.scripps.edu>
> Sent: Wednesday, July 11, 2007 6:14 AM
> Subject: Re: AMBER: Could not find cntrl namelist
>
>
> > Please, see below.
> > --- "M. L. Dodson" <mldodson.houston.rr.com> wrote:
> >
> >> Francesco Pietra wrote:
> >> > Hi Ross:
> >> > I'll study your suggestions below, which arrived when I had decided to
> >> simplify
> >> > the problem by running equatorial methylcyclohexane, prepared for xleap
> >> with
> >> > antechamber. The same issue "Could not find cntrl namelost" arose.
> >> >
> >> > This time, contrary to all previous experience, I could quit the xleap
> >> window
> >> > without getting the "not saved" message. Contrary to my hope, it didn't
> >> > anticipate the solution.
> >> >
> >> > I also run my eqeq molecule with different mdin, always getting the
> >> > "Could
> >> not
> >> > ..." error message.
> >> >
> >> > Attached are all relevant files.
> >> >
> >> > Thanks
> >> >
> >> > francesco pietra
> >> >
> >> >
> >>
> >> This input file runs fine for me.
> >
> > Do you mean the preliminary minimization (which runs fine for me, too), or
> > the
> > subsequent MD? (which is where I get the error message).
> >
> >> I think your sander compilation
> >> must be bogus somehow. I'm using sander compiled with g95.
> >
> > I installed Amber9 serial (to begin with) on debian linux amd64 etch.
> > Compilers
> > used were ifort_x86_64 (that I indicated) and gcc (that was used
> > automatically;
> > now that machine is switched off, can't verify the version, though is
> > surely an
> > updated one; I never installed g95). Sander failed to compile static (as I
> > was
> > indicated to do), then I switched to dynamic, it compiled and all tests
> > passed
> > without errors.
> >
> > I had previously installed openmpi and libnuma, though parallelization was
> > not
> > carried out (planned with all intel compilers).
> >
> > Can you suggest an extra test for sander serial?
> >
> > Thanks
> >
> > francesco pietra
> >
> >>
> >> Bud Dodson
> >>
> >> PS, where did you get the mdinfo file? I got one that differs
> >> only in the number of steps, 272 vs. 274 (and everything else on
> >> the NSTEP data line, but differs only in the last few decimal
> >> places).
> >>
> >> >
> >> >
> >> > --- Ross Walker <ross.rosswalker.co.uk> wrote:
> >> >
> >> >> Hi Francesco,
> >> >>
> >> >>> What I fear at this point is related to what I posted
> >> >>> yesterday about a remind
> >> >>> by David Case that antechamber treats single residues:
> >> >> The issue is that the only possible things that could be generating
> >> >> this
> >> >> error message is either there is something wrong with the mdin file,
> >> >> the
> >> >> incorrect file was specified with -i or there is some issue with read
> >> >> permissions of the mdin file. At this point in the code the prmtop
> >> >> file
> >> >> hasn't even been opened so it cannot be related to a problem with
> >> >> that.
> >> >>
> >> >> Could you please attach your mdin file to an email (as an actual
> >> attachment)
> >> >> direct from the copy on the machine on which you are having problems.
> >> >> If
> >> you
> >> >> have to ftp it to another machine to email it then make sure you
> >> >> select
> >> >> binary format for the transfer. Then we can take a look and see if
> >> >> there
> >> is
> >> >> something weird going on.
> >> >>
> >> >> Another option you could try as well is to create a brand new file on
> >> >> the
> >> >> machine on which you are running sander and explicitly type in, on
> >> >> that
> >> >> machine in vi, everything you want in the input file. That way you
> >> >> work
> >> >> around any kind of weird corruption and/or strange control characters
> >> >> that
> >> >> may have made it into the old file during the copying / cut / pasting
> >> >> etc.
> >> >>
> >> >> Seeing the exact input file as sander sees it on your machine will
> >> >> really
> >> >> help.
> >> >>
> >> >> All the best
> >> >> Ross
> >> >>
> >> >> /\
> >> >> \/
> >> >> |\oss Walker
> >> >>
> >> >> | HPC Consultant and Staff Scientist |
> >> >> | San Diego Supercomputer Center |
> >> >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> >> >> | http://www.rosswalker.co.uk | PGP Key available on request |
> >> >>
> >> >> Note: Electronic Mail is not secure, has no guarantee of delivery, may
> >> >> not
> >> >> be read every day, and should not be used for urgent or sensitive
> >> >> issues.
> >> >>
> >> >>
> >> >> -----------------------------------------------------------------------
> >> >> The AMBER Mail Reflector
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> >> >>
> >> >
> >> >
> >> >
> >> >
> >> >
> >>
> >
>
____________________________________________________________________________________Ready
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> >>
> >> --
> >> M. L. Dodson
> >> Email: mldodson-at-houston-dot-rr-dot-com
> >> Phone: eight_three_two-five_63-386_one
> >> -----------------------------------------------------------------------
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> >
>
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Received on Sun Jul 15 2007 - 06:07:08 PDT
