Dear Amber Users,
I have successfully produced snapshots from a
trajectory using the mm_pbsa command. However, now I
am trying to do a "stability" calculation, using those
snapshots. I have an input file modelled on the
Example02 in /amber7/src/mm_pbsa/Examples.
Immediately after I execute the command, I get the
error message:
"Can't use an undefined value as an ARRAY reference at
/apps/amber/amber7/src/mm_pbsa/mm_pbsa_statistics.pm
line 1234."
My rather short resulting log file reads:
=>> Init data
Presuming executables of amber suite to be in
/apps/amber/amber7/exe
=>> Reading input parameters
Found PREFIX => ras_raf_II_wt
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./good.top
Found RECPT => ./receptor.top
Found LIGPT => ./ligand.top
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 0
Found FOCUS => 0
Found INDI => 1.0
Found EXDI => 80.0
Found PERFIL => 80.0
Found SCALE => 2
Found LINIT => 1000
Found BNDCON => 4
Found CHARGE => ../my_amber94_delphi.crg
Found SIZE => ../my_parse_delphi.siz
Found SURFTEN => 0.00542
Found SURFOFF => 0.092
Found IGB => 4
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 1.4
Found RADII => ../atmtypenumbers
Found DELPHI => /apps/amber/DIST/LINUX/delphi
=>> Checking sanity
Checking GENERAL
Checking MM
Checking DELPHI
Checking GB
Checking MS
=>> Creating input
Sander input
Delphi input
=>> Calculating energy / entropy contributions
=>> Doing statistics
=>> Values of global variables
TEMP = 300
R = 8.314
gammaP = 0.00542
betaP = 0.092
gammaG = 0.0072
betaG = 0.00
=>> Reading input
=>> Reordering files
Final order:
1. ras_raf_II_wt_com.all.out: -
2. ras_raf_II_wt_rec.all.out: -
3. ras_raf_II_wt_lig.all.out: -
=>> Reading files
Reading ras_raf_II_wt_com.all.out
Reading ras_raf_II_wt_rec.all.out
Reading ras_raf_II_wt_lig.all.out
=>> Treat special parameters
My molecular complex is the DNA decamer from the first
tutorial, and my receptor and ligand are opposite
strands.
Can anyone tell me how to fix this problem? Do I need
to adjust the mdread.f file, and if so, how?
Thanks for any input,
Peter Anderson
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Received on Fri Jun 20 2003 - 23:53:01 PDT
