Dear Amber Team
i am using mm_pbsa in determining the binding energy and i made the snapshot
step with out any errors but when i tried calculation of the energy i got
this error:
=>> Init data
Presuming executables of amber suite to be in
/usr/local/Amber/Amber11/serial-gnu/amber11/bin
=>> Reading input parameters
Found PREFIX => trial_1
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./1KPV_complex_wo_salt.top
Found RECPT => ./1KPV_all_acceptor_wo_salt.top
Found LIGPT => ./1KPV_all_ligand_wo_salt.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 PROC => 2
Found REFE => 0
Found INDI => 1.0
Found EXDI => 80.0
Found SCALE => 4.0
Found LINIT => 500
Found PRBRAD => 1.6
Found RADIOPT => 0
Found FOCUS => 0
Found PERFIL => 80.0
Found CHARGE => ./my_amber94_delphi.crg
Found SIZE => ./my_parse_delphi.siz
Found SURFTEN => 0.005
Found SURFOFF => 0.0
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found INTDIEL => 1.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 0.0
Found DELPHI => /home/gohlke/src/delphi.98/exe/delphi
=>> Checking sanity
Checking GENERAL
Setting START to default 1
Setting STOP to default 10e10
Setting OFFSET to default 1
Setting VERBOSE to default 0
Setting PARALLEL to default 0
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
Use of uninitialized value $inp in concatenation (.) or string at
/usr/local/Amber/Amber11/serial-gnu/amber11/src/mm_pbsa/
mm_pbsa_createinput.pm line 596.
Use of uninitialized value $inp in concatenation (.) or string at
/usr/local/Amber/Amber11/serial-gnu/amber11/src/mm_pbsa/
mm_pbsa_createinput.pm line 596.
Use of uninitialized value $inp in concatenation (.) or string at
/usr/local/Amber/Amber11/serial-gnu/amber11/src/mm_pbsa/
mm_pbsa_createinput.pm line 596.
=>> Calculating energy / entropy contributions
Calc contrib for ./trial_1_com.crd.1
Checking atom numbers
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
/usr/local/Amber/Amber11/serial-gnu/amber11/bin/sander -O -i
pbsa_com.in -o pbsa_com.1.out -c ./trial_1_com.crd.1 -p
./1KPV_complex_wo_salt.top not successful
For details see:
http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
Best Regards,
*Esam *
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Received on Mon Aug 22 2011 - 05:00:03 PDT
