From: bo baker (bo.bybaker_at_gmail.com)
Date: Tue Jun 13 2006 - 14:16:56 CDT
Hi, Michael, Leonardo and Raymond:
Thank you for correcting my mistake with -bash. I try the commands as
you suggested. The 'export' command went through, but there comes
other problem. Here is how I did:
~bakerby$ cd /Applications/NAMD_2.6b1_MacOSX-PPC
Peds-HSE1401-ML1:/Applications/NAMD_2.6b1_MacOSX-PPC
~bakerby$ export DYLD_LIBRARY_PATH='/Applications/NAMD_2.6b1_MacOSX-PPC'
~bakerby$ /Applications/NAMD_2.6b1_MacOSX-PPC/namd2 PBR1-vm061006.conf
> test.log &
Here is the error message:
Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Simulation config file is not accessible.
Charm++ fatal error:
FATAL ERROR: Simulation config file is not accessible.
I look at the files in /NAMD_2.6b1_MacOSX-PPC, the
'PBR1-vm061006.conf' file is there. Why it is not accessible?
The NAMD_2.6b1_MacOSX-PPC was installed in the computer previously.
The computer was crushed. After it was repaired, I move the whole
folder of 'NAMD_2.6b1_MacOSX-PPC' into the new hard drive where is the
operation system loacted. I am not sure if this has something to do
with the running problem. Do I need to re-install the program into the
new hard drive? If so, do I have to install fftw, tcl, and BM XL C/C++
Run-Time Library again?
Here is the files in the 'NAMD_2.6b1_MacOSX-PPC':
FFTW_NAMD_2.6b1_MacOSX-PPC.txt
flipdcd
PBR
lib
libibmc++.A.dylib
license.txt
log
PBR1-vm061006.conf
namd2
namdplot
notes.txt
PBRtest061006.log
opt
README.txt
par_all27_prot_lipid.inp
announce.txt
par_all27_prot_lipid.prm
charmd
charmd_faceless
test.log
charmrun
top_all27_prot_lipid.inp
common
conf
flipbinpdb
Thank you very much for your suggestions.
Bo
On 6/13/06, Raymond C. Fort Jr. <rcfort_at_maine.edu> wrote:
> At 04:55 PM 6/12/2006 -0700, you wrote:
> >Hi, NAMD:
> >
> >I have a problem to run MD in the Mac computer. Here is how I did:
> >
> >~ bakerby$ cd /Applications/NAMD_2.6b1_MacOSX-PPC
> >bakerby$ setenv DYLD_LIBRARY_PATH /Applications/NAMD_2.6b1_MacOSX-PPC
> >
> >Here is the error message:
> >
> >-bash: setenv: command not found
> >
> >Without setting the library, namd does not run. Can any one suggest me
> >what could be wrong, and how can I fix it? I use Mac OSX 10.4.
> >
> >Thank you.
> >
> >Bo
>
> In the bash shell, you need to export environment variables, rather than
> setting them.
>
>
>
> Professor Ray Fort Jr. rcfort_at_maine.edu
> Department of Chemistry chemistry.umeche.maine.edu/fort.html
> University of Maine Voice: (207)-581-1180
> Orono, ME 04469 FAX: (207)-581-1191
>
> Computer modeling of organic and biomolecules; chemistry of lignin and
> cellulose
>
>
>
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