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 *
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 05 2011 - 14:30:03 PDT
