From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Fri Dec 23 2005 - 02:56:34 CST
Ok...sorry.
I should check things more carefully at 4am. My .psf and .pdb file names
didn't match up with my configuration file.
Josh
On Fri, December 23, 2005 3:53 am, Joshua D. Moore wrote:
> All,
>
> This is an error I have never seen before, and I haven't found any reports
> on the mailing list. My .psf file is indeed large, > 13 MB. It seems
> fine when I open it with vi. Is this a memory issue with the computer?
>
> Below is the error I am seeing. Why is it trying to zip the file? Is
> NAMD trying to zip the file?
>
> Thanks.
>
> Josh
>
> Info: SUMMARY OF PARAMETERS:
> Info: 13 BONDS
> Info: 22 ANGLES
> Info: 32 DIHEDRAL
> Info: 0 IMPROPER
> Info: 11 VDW
> Info: 0 VDW_PAIRS
> Command = zcat 2C4E1_125_45458.psf.gz.Z
> Filename.Z = 2C4E1_125_45458.psf.gz.Z
> Command = gzip -d -c 2C4E1_125_45458.psf.gz.gz
> Filename.gz = 2C4E1_125_45458.psf.gz.gz
> FATAL ERROR: UNABLE TO OPEN .psf FILE 2C4E1_125_45458.psf.gz
> PC: 0xb18ca40 MPI_SGI_stacktraceback in /usr/lib64/libmpi.so
> PC: 0xb1b5e30 PMPI_Abort in /usr/lib64/libmpi.so
> PC: 0x105ef8c8 CmiAbort in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x100a4f2c NAMD_die(const char*) in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x103683d4 Molecule::read_psf_file(char*,Parameters*) in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x103650b8 Molecule::Molecule(SimParameters*,Parameters*,char*) in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x10385588 NamdState::configListInit(ConfigList*) in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x10401110 ScriptTcl::initcheck(void) in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x10402170 ScriptTcl::Tcl_minimize(void*,Tcl_Interp*,int,char**) in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x1062d318 TclInvokeStringCommand in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
> PC: 0x10679a6c EvalObjv in
> /nas/ncsu/moorejd/NAMD_2.6b1_Origin2000-MPI/namd2
>
>
--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
--------------------------------------------------
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