AMBER Archive (2007)

Subject: Re: AMBER: Could not find cntrl namelist

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Jul 11 2007 - 05:14:51 CDT

Please, see below.
--- "M. L. Dodson" <mldodson_at_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_at_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_at_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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