My suggestion is to download the latest Ambertools and start from
there ... it's better supported ...
All the best,
Ray
On Sat, Nov 5, 2011 at 9:27 AM, 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 => snapshot
> Found PATH => ../01_GenerateSnapshots/
> Found COMPLEX => 1
> Found RECEPTOR => 1
> Found LIGAND => 1
> Found COMPT => /people/home/binding_energy/02_trial/complex/complex.top
> Found RECPT =>
> /people/home/binding_energy/02_trial/acceptor/acceptor.top
> Found LIGPT =>
> /people/home/binding_energy/02_trial/ligand/correct_ligand.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 => 2.0
> 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 ../01_GenerateSnapshots/snapshot_com.crd.1
> Checking atom numbers
> Calc MM/GB/SAS
> Generate PDB
> /usr/local/Amber/Amber11/serial-gnu/amber11/bin/ambpdb -p
> /people/home/eabualrous/binding_energy/02_trial/complex/3CCH_bp_wt_w_EGSRNQDWL_correct_complex.top
> < ../01_GenerateSnapshots/snapshot_com.crd.1 > tmp.pdb.1 2> /dev/null not
> successful
> For details see:
> http://ambermd.org/Questions/mm_pbsa.html#gen_pdb_command_not_successful
>
> *Best Regards,
> Esam *
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Sat Nov 05 2011 - 14:30:03 PDT
