AMBER Archive (2003)

Subject: mm_pbsa problem

From: Peter Anderson (toutvabien78_at_yahoo.com)
Date: Fri Jun 20 2003 - 17:31:17 CDT

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

__________________________________
Do you Yahoo!?
SBC Yahoo! DSL - Now only $29.95 per month!
http://sbc.yahoo.com