--- Francesco Pietra <chiendarret.yahoo.com> wrote:
> Date: Wed, 11 Jul 2007 14:50:37 -0700 (PDT)
> From: Francesco Pietra <chiendarret.yahoo.com>
> Subject: Re: AMBER: Could not find cntrl namelist
> To: amber.scripps.edu
>
> Hi Robert:
> The command line was just the one indicated here. However, the RST file at -c
was badly
> named "eqmecyl_vac_min.rst" . Once corrected to "eqmecycl_vac_min.rst", for
> analogy with the other files and to correspond to the command line, the house
> is finally in order.
>
> Thanks a lot
>
> francesco
>
> --- Robert Duke <rduke.email.unc.edu> wrote:
>
> > Hi Francesco -
> > The error says the file with logical unit # 9 cannot be found - that is the
>
> > inpcrd, or restrt file specified with the -c option. What you showed in
> the
> > command line, and what the mdout shows, are different, so that is NOT the
> > command you entered. Track down the right incprd/restrt, make sure it is
> in
> > the current working directory with everything else, and specify it with -c.
> > Regards - Bob Duke
> >
> > ----- Original Message -----
> > From: "Francesco Pietra" <chiendarret.yahoo.com>
> > To: <amber.scripps.edu>
> > Sent: Wednesday, July 11, 2007 11:10 AM
> > Subject: Re: AMBER: Could not find cntrl namelist
> >
> >
> > > 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.
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > -----------------------------------------------------------------------
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> > >> >> >
> > >> >> >
> > >> >> >
> > >> >> >
> > >> >>
> > >> >
> > >>
> > >
> >
>
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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 - 06:07:12 PDT
