Re: AMBER: Could not find cntrl namelist

From: David A. Case <case.scripps.edu>
Date: Tue, 10 Jul 2007 16:04:15 -0700

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. 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.

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


          -------------------------------------------------------
          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).

....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jul 11 2007 - 06:07:53 PDT
Custom Search