Re: [AMBER] Error in mm_pbsa

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 22 Aug 2011 19:58:07 +0800

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
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