AMBER Archive (2003)

Subject: Re: mm_pbsa problem

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Fri Jun 20 2003 - 20:47:21 CDT

Peter Anderson wrote:
>
> 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
                      ^^^^^^^^^^^^^

You need to replace this with the proper prefix for your molecule files.
The naming scheme mm_pbsa uses when generating and reading coordinates
is prefix_{com,rec,lig}.crd.<a number> .

Best regards

Holger

> 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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-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++