Dear Ross:
Although I did not remark again the point in my last email with attachments, my
installation of Amber9 (serial at the moment) was also able to run successfully
the minimization (I called it "relaxing") you have run with the files I
provided in attachment. If you look at my previous emails (see below)
concerning molecule eqeq, you can also see that that command line for
preliminary minimization ended successfully.
The issue came (with both eqeq previously and equatorial methylcyclohexane now)
at next procedure, MD, the one with command line:
$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.mdcrd
for which I provided in my last email relevant files: vac_md1_12Acut.in for
mdin; eqmecycl_vac_md1_12Acut.out for the resuly; no mdcrd was generated, of
course.
__________
Here, within asterisks, I reproduce my first email on this issue:
*****************************
With Amber9 I am applying the scripts of web Tutorial 1B (polyA-polyT) to
another case. While the tutorial run OK, and the new case also run OK up to
section 4, relaxing structure before MD, the MD itself, with command line:
$AMBERHOME/exe/sander -O -i eqaeqb_gb_md1_12Acut.in -o eqaeqb_gb_md1_12Acut.out
-c eqaeqb_gb_init_min.rst -p eqaeqb.prmtop -r eqaeqb_gb_md1_12Acut.rst -x
eqaeqb_gb_md1_12Acut.mdcrd
did not run, tail -f telling:
"Could not find cntrl namelist"
File "eqaeqb_gb_md1_12Acut.in" reads:
# eqaeqb MD Generalised Born, 12 angstrom cut off
&cntrl
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 100000, dt = 0.001,
cut = 12.0
/
***************************
To conclude, I am surely doing something wrong, though I am unable to see
where. I must also add (in relationship to another email I received) that I
regret very much for all troubles I caused. I wish not to bother the audience
any longer on this issue, in the fear that I am doing something silly that
leads other people to waste their time. I'll try to come out alone.
Thanks
francesco pietra
--- Ross Walker <ross.rosswalker.co.uk> wrote:
> 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.
> > >
> > >
> > >
> > --------------------------------------------------------------
> > ---------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
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> > >
> >
> >
> >
> >
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Received on Sun Jul 15 2007 - 06:07:08 PDT
