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
Received on Tue Jul 01 2003 - 20:53:01 PDT
