Hi Ross:
No sign of DOS formatting. There is no Windows installed here, so that the
problem you pointed out (thanks a lot for that!) should have not arisen. At any
event, vi does not show any sign of DOS, as far as I can understand: no ^M, and
the last line is
"filename" 9L, 227 9,1 All
on amd64
and
"filename" 9L, 228C 1,1 All
on i386
(both debian linux etch).
I have installed "tofrodos" debian package, and command
dos2unix <filename>
did not alter the above affairs and a new attempt at running sander resulted in
the same failure.
What I fear at this point is related to what I posted yesterday about a remind
by David Case that antechamber treats single residues:
=====================================================
I have treated with Amber9/Antechamber a molecule (natural product, 98 atoms)
made of two residues (because I had used another suite of programs to calculate
RESP charges, which required to make smaller residues, and pdb atom names were
correct).
I expected failure of antechamber. Actually, it prepared valid parameter and
coordinate files, that allowed correct minimizations."list" on the prepin file
showed as new unit the first of the two residues, in three capital letters. At
all stages, generation of pdb files gave the correct molecule on VMD.
Perhaps what I did is not the equivalent of what is warned about here, although
my molecule is seen as two residues on the original suite where the arrangement
was done.I have treated with Amber9/Antechamber a molecule (natural product, 98
atoms)
made of two residues (because I had used another suite of programs to calculate
RESP charges, which required to make smaller residues, and pdb atom names were
correct).
I expected failure of antechamber. Actually, it prepared valid parameter and
coordinate files, that allowed correct minimizations."list" on the prepin file
showed as new unit the first of the two residues in three capital letters
[added now: i.e., EQA for the case at issue]. At all stages, generation of pdb
files gave the correct molecule on VMD.
Perhaps what I did is not the equivalent of what is warned about here, although
my molecule is seen as two residues on the original suite where the arrangement
was done.
=======================================
I wonder whether such an initial two-residues pdb file, treated by antechamber,
may have lead to correct minimizations, while MD itself failed, warning "Could
not find cntrl namelist".
I plan to re-do everything from the original pdb file for the molecule not cut
into fragments. Also because this belongs to a family of undescribed compounds
that can't be put on internet at this stage.
Thanks
francesco
--- Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Francesco,
>
> If you have the command on you Unix installation can you try running:
>
> dos2unix eqaeqb_gb_md1_12Acut.in
>
> if the mdin file is a dos formatted text file and you try to use it on a
> unix machine you'll see these types of errors. This can often happen if you
> download a text file onto a windows desktop and/or create / edit on a
> windows desktop and then copy it over to the unix machine. The dos2unix
> command should strip all the erroneous line feeds from the end of the text
> file (which cat / tail etc don't show) and then hopefully things should
> work.
>
> Note, if you open the input file with vi it should report at the very bottom
> of the screen the text format - try it on your input file and see if it
> reports dos format. You'll probably also see a load of purple ^M's at the
> end of each line.
>
> If that doesn't work please attach the mdin, prmtop and inpcrd files to an
> email.
>
> 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: Monday, July 09, 2007 13:54
> > To: amber.scripps.edu
> > Subject: Re: AMBER: Could not find cntrl namelist
> >
> > No blank line before the one starting with #, and formatting
> > was exactly as in
> > tutorial 1B. Now corrected by adding a comma after 300.0 (I
> > find this curious
> > because I was able to run that tutorial 1B).
> >
> > On trying to run sander, same error. Attached is the out
> > file. Of course the
> > mdcrd file was not generated.
> >
> > Any time feasible I cut and paste on posting. Sometimes
> > uneasy, when, as for
> > tail -f, the outcome is printed on the terminal window of
> > the machine where
> > amber9 is installed, while I am at a desktop scp linked to
> > the computing
> > machine (VMD is on this desktop).
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> >
> > --- "M. L. Dodson" <mldodson.houston.rr.com> wrote:
> >
> > > Francesco Pietra wrote:
> > > > 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
> > > > /
> > > > -------------
> > > >
> > > > A google search did not clarify the problem. As a
> > newcomer to MD I
> > > apologize
> > > > for posting trivial questions, if this is the case.
> > > > Thanks
> > > >
> > > > francesco pietra
> > > >
> > > >
> > >
> > > One of the most common cause of this kind of problem seems to be
> > > formatting problems. Be sure there is no blank line before the
> > > one starting with '#'. Also, all entries in the namelist list
> > > should be separated from the rest by a comma. I notice temp0 does
> > > not conform. I'm unclear about the last line: cut = 12.0, but I
> > > always end the last line with a comma as well. The error message
> > > seems to indicate a slightly different problem, but check these
> > > items and try again. Be sure you cut and paste when sending files
> > > or parts of files to the list.
> > >
> > > Bud Dodson
> > > --
> > > M. L. Dodson
> > > Email: mldodson-at-houston-dot-rr-dot-com
> > > Phone: eight_three_two-56_three-386_one
> > >
> > --------------------------------------------------------------
> > ---------
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> > >
> >
> >
> >
> >
> >
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Received on Wed Jul 11 2007 - 06:07:48 PDT
