Can you email me off the list, the file "pbsa_com.1.out"? It's really
hard to understand what's going on only with the info in the log file
...
All the best,
Ray
On Mon, Aug 22, 2011 at 7:38 PM, Esam Tolba <eatolba.gmail.com> wrote:
> 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 *
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 22 2011 - 05:00:04 PDT
