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 *
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Aug 22 2011 - 06:00:03 PDT
