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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Received on Tue Jun 24 2003 - 17:53:01 PDT
