2011/5/7 Andrew Voronkov <drugdesign.yandex.ru>
> Yes, sure, just copied wrong line, but anyway with that line seems like
> there is no problems, nothing is reported. But I get an error it when run
> mmpbsa_energy.pl script:
>
> sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
> ./39981.prmtop not successful
>
It appears as though this is the full command you're trying to enter. Thus,
it is parsing "not" as a flag, which it doesn't recognize. Take out "not
successful" and rerun it.
> here is the log, looks normal:
>
> =>> Init data
> Presuming executables of amber suite to be in
> /home/osolodkin/amber10/exe
>
> =>> Reading input parameters
> Found PREFIX => snapshot
> Found PATH => ./
> Found COMPLEX => 1
> Found RECEPTOR => 1
> Found LIGAND => 1
> Found COMPT => ./39981.prmtop
> Found RECPT => ./1ijynow.prmtop
> Found LIGPT => ./39981g.prmtop
> 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
> Found LINIT => 1000
> Found PRBRAD => 1.4
> Found ISTRNG => 0.0
> Found RADIOPT => 0
> Found NPOPT => 1
> Found CAVITY_SURFTEN => 0.0072
> Found CAVITY_OFFSET => 0.00
> Found SURFTEN => 0.0072
> Found SURFOFF => 0.00
> 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
>
> =>> Checking sanity
> Checking GENERAL
> Setting START to default 1
> Setting STOP to default 10e10
> Setting OFFSET to default 1
> Setting VERBOSE to default 0
> Checking MM
> Checking PB
> Checking GB
> Checking MS
>
> =>> Creating input
> Sander input
> PBSA input
>
> =>> Calculating energy / entropy contributions
> Calc contrib for ./snapshot_com.crd.1
> Calc MM/GB/SAS
>
What's the problem here?
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat May 07 2011 - 12:00:02 PDT
