Re: [AMBER] Error in mm_pbsa

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 22 Aug 2011 20:31:13 +0800

Okay, based on your attached output file. It seems that your computer
does not have enough memory for you to run mmpbsa with such a small
grid spacing ... please change scale from 4 to 2 and try again ...

All the best,
Ray

On Mon, Aug 22, 2011 at 8:12 PM, Esam Tolba <eatolba.gmail.com> wrote:
>
> THanks for help
>
>
> ---------- Forwarded message ----------
> From: Ray Luo, Ph.D. <ray.luo.uci.edu>
> Date: Mon, Aug 22, 2011 at 1:58 PM
> Subject: Re: [AMBER] Error in mm_pbsa
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> 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 *
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Aug 22 2011 - 06:00:03 PDT
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