AMBER Archive (2003)

Subject: input problem

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Tue Jul 01 2003 - 14:12:23 CDT

Hi there...

I'm new to amber and I've been trying to run some tests, but I'm not
being successful even at that.
I have generated the prep file successfully with antechamber using gaff
and AM1-BCC method. With that file I have generated successfully ( at
least it looks so ) the coordinate and topology file with Leap.
But sander does not runs successfully.
It seems it complains about the namelist, but it's quite similar to the
ones found in /usr/local/amber7/test.

Take a look. This is my md0.in file:

  alpha-ciclodextrina isolada a temperatura ambiente (equilibracao)
 &cntrl
    IMIN=0, IREST=0,
    NTWX=100, NTWV=100,
    NTWE=100, NTSLIM=5000,
    NTB=0, NSCM=100, NTPR=50,
    NTC=1, NTX=1, IREST=0,
    NTT=1, TEMP0=298.15, TAUTP=1.0,
 &end

Note that characters begin in second or later column.

When I use the command:

sander -i md0.in -o md0.out -p alphacd.top -c alphacd.crd -x md0.crd -v
md0.vel -e md0.en -O &

it returns the following:

namelist read: variable not in namelist
apparent state: unit 5 named md0.in
last format: list io
lately reading sequential formatted external IO

and aborts. It reads ( apparently ) successfully the md0.in file, for
the md0.out file is written with the following:

          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Tue Jul 1 15:32:36 2003

  [-O]verwriting output

File Assignments:
| MDIN:
md0.in
| MDOUT:
md0.out
|INPCRD:
alphacd.crd
| PARM:
alphacd.top
|RESTRT:
restrt
| REFC:
refc
| MDVEL:
md0.vel
| MDEN:
md0.en
| MDCRD:
md0.crd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip

 Here is the input file:

  alpha-ciclodextrina isolada a temperatura ambiente
(equilibracao)
 &cntrl

    IMIN=0,
IREST=0,
    NTWX=100,
NTWV=100,
    NTWE=100,
NTSLIM=5000,
    NTB=0, NSCM=100,
NTPR=50,
    NTC=1, NTX=1,
IREST=0,
    NTT=1, TEMP0=298.15,
TAUTP=1.0,
 &end

                                                                               

                                                                               

Don't know what it can be... any help is very welcome.
Thanks in advance
Herbert