AMBER Archive (2003)

Subject: Re: Another mm_pbsa problem

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Jun 24 2003 - 12:08:25 CDT

Peter Anderson wrote:
>
> Dear Amber Users,
>
> I am trying to do a mm_pbsa stability calculation
> based on a number of different snapshots.
>
> Immediately after I enter the command % mm_pbsa.pl
> mm_pbsa.in > log.out, however, I get the following
> error message:
>
> Unit 6 Error on OPEN: sander_com.1.out
>
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> /apps/amber/amber7/exe/sander -O -i
> sander_com.in -o sander_com.1.out -c
> ./ras_raf_II_wt_com.crd.1 -p ./ras_raf_II_wt.prmtop
> not successful

mm_pbsa by default calls sander assuming that this is the non-parallel
version of the program. In your case it looks as if
/apps/amber/amber7/exe/sander is the parallel version. Try specifying in
the @PROGRAMS part of the mm_pbsa.in file a line such as "SANDER
mpirun -np 1 /apps/amber/amber7/exe/sander". Alternatively, you can
(re)compile sander as non-parallel version and then specify the location
of this version as "SANDER <non-par sander>".

Best regards

Holger

>
> There is no sander_com.1.out file in my directory
> after I enter the command. Am I correct in assuming
> that the program is looking for this file and cannot
> find it?
>
> My resulting output file is the following:
>
> =>> 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 => ./ras_raf_II_wt.prmtop
> Found RECPT => ./ras_II_wt.prmtop
> Found LIGPT => ./raf_wt.prmtop
> 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
> Calc contrib for ./ras_raf_II_wt_com.crd.1
> Calc MM/GB/SAS
> p0_17307: p4_error: : 1
>
> Does anyone know how I can fix this problem?
>
> Thank you very much,
> 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
+++++++++++++++++++++++++++++++++++++++++++++