Re: AMBER: Could not find cntrl namelist

From: Francesco Pietra <chiendarret.yahoo.com>
Date: Tue, 10 Jul 2007 23:48:41 -0700 (PDT)

--- "David A. Case" <case.scripps.edu> wrote:

> On Tue, Jul 10, 2007, Francesco Pietra wrote:
>
> > 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.
>
> I hope you realize that this all very frustrating to people who are trying to
> help you.

Please, see my email of reply to Ross Walker: I decided to try to come out with
my own means from this problem. Bothering people is the last I would like to
do.


>Once again: the failure to find the cntrl namelist has nothing to
> do with what molecule you are running, what you did with xleap or
> antechamber,
> or anything like that.

This just why I run the procedures with equatorial methylcyclohexane. This
indicated to me, too, that the problem is not bound to my eqeq molecule (or not
to it alone).

> One of the files you attached was called eqmecycl_vac_md1_12Acut.out. Did
> you
> look closely at this? Here is what I see:

This was the crucial file that I had not attached if it had not attracted my
attention. I see below, though, on opening with vi the attachment I sent with
my email (downloaded from the yahoo server) I do not see the "strange"
characters that you have seen and report below.
>
>
> -------------------------------------------------------
> Amber 9 SANDER 2006
> -------------------------------------------------------
>
> | Run on 07/10/2007 at 22:53:17
> [-O]verwriting output
>
> File Assignments:
> | MDIN: vac_md1_12Acut.in
> | MDOUT: eqmecycl_vac_md1_12Acut.out
> |INPCRD: eqmecycl_vac_min.rst
> | PARM: eqmecycl.prmtop
> |RESTRT: eqmecycl_vac_md1_12Acut.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: eqmecycl_vac_md1_12Acut.mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
>
> Here is the input file:
>
> #eqaeqb MD generalized Born, 12 angstrom cutoff
> | &cntrl
> | imin = 0, ntb = 0,
> | igb = 0, ntpr = 100, ntwx = 100,
> | ntt = 3, gamma_ln = 1.0,
> | tempi = 300.0, temp0 = 300.0,
> | nstlim = 100000, dt = 0.001,
> | cut = 12.0
> | /
> Could not find cntrl namelist
>
>
> Before the last line, the program is just copying the input file you
> provided,
> so you can see what you asked the program to do. Note the two characters at
> the beginning of the lines with cntrl namelist: those are your problem. They
> are coming from the input file itself (which as far as I can see, you did not
> attach to your email; there was an input file attached, but it was clearly
> from some different job).
>

Yes, sometimes these affairs become frustrating. Therefore, I organized for
tomorrow training of my pointing dog on chukars (Alectoris chukar) on the
highhills (you may have a look at my second - or first - interest, ie, the
psychology of the pointing dog and game, as in my tale on Gray's Sporting
Journal, volume thirthy, issue 4, August 2005. A non relaxed pointing dog can't
do any good job, so it is of myself.

Warm regards to all

francesco pietra


> ....dac
>
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Received on Sun Jul 15 2007 - 06:07:03 PDT
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