RE: AMBER: Could not find cntrl namelist

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 10 Jul 2007 14:57:39 -0700

Dear Francesco

I can find nothing wrong with your input files so am at a complete loss to
explain the problem you are seeing. Here is what I tried on my machine. This
is a Intel Pentium-D running RHEL 4, Amber 9 patched to bugfix.36, compiled
in serial with ifort 9.1.039 and MKL 8.0.2.

I saved your vac_min.in, eqmecycl.prmtop and eqmecycl.inpcrd files directly
from your email to my home directory and then ran sander with:

/usr/local/amber9/exe/sander -O -i vac_min.in -o vac_min.out -p
eqmecycl.prmtop -c eqmecycl.inpcrd -r vac_min.rst

And it ran in 0.03 seconds stopping the minimization after 274 steps when
the convergence criteria had been met. Attached are all of the files I used
/ were produced in this run.

Hence I cannot explain why you see the problems you do - are you running
this with the serial version of Amber, interactively on your machine? Are
are you submitting this to a queuing system / using the parallel version?

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.

> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Francesco Pietra
> Sent: Tuesday, July 10, 2007 14:12
> To: amber.scripps.edu
> Subject: RE: AMBER: Could not find cntrl namelist
>
> 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
>
>
>
>
> --- 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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Received on Wed Jul 11 2007 - 06:07:55 PDT
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