AMBER Archive (2003)

Subject: Another mm_pbsa problem

From: Peter Anderson (toutvabien78_at_yahoo.com)
Date: Tue Jun 24 2003 - 11:47:58 CDT

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

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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