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.
>> >> >>
>> >> >>
>> >> >> -----------------------------------------------------------------------
>> >> >> The AMBER Mail Reflector
>> >> >> To post, send mail to amber.scripps.edu
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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
