Hi Robert:
The command line was just the one indicated here. However, the mdin 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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> >
>
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Received on Sun Jul 15 2007 - 06:07:12 PDT
