sander_com.in and sander_com.1.out are files automatically created by
mm_pbsa.pl during the MMPBSA calculation, so they are not files that you
need place in a directory. Was sander_com.1.out created? If so, this could
possible have a more informative error message in it as to why the
calculation terminated on the first snapshot.
-Bill
On Tue, May 18, 2010 at 1:49 AM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> Probably because I've use rich text formatting. I've use plain text now, so
> it shoul be readable now.
>
> Dear Amber users, I have problems with binding energy calculation using
> binding_energy.mmpbsa.
> The snapshots seem to be extracted correctly with the appriopriate names
> (2770 snapshots).
>
> "[voronkov.t60-2 PM-CAP-1IJYCAP]$ $AMBERHOME/exe/mm_pbsa.plbinding_energy.mmpbsa > binding_energy.log
> /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o
> sander_com.1.out -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not
> successful
> [voronkov.t60-2 PM-CAP-1IJYCAP]$
> /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out
> -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful
> "
>
> maybe I need to place these files sander_com.in -o sander_com.1.out
> locally, but I haven't found them in the tutorial?
> The log is in the bottom, but seems not to be very informative, probably
> some problems with files names or command flags order?
>
> Sincerely yours,
> Andrew
>
>
> =>> 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 => ./1ijy-pmc_v.prmtop
> Found RECPT => ./1ijy_v.prmtop
> Found LIGPT => ./pmc_v.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
>
> 16.05.10, 15:40, "Jason Swails" <jason.swails.gmail.com>:
>
> > Hello,
> >
> > All I got was garbled markup language. Can you re-send without it?
> >
> > All the best,
> > Jason
> >
> > On Sun, May 16, 2010 at 6:53 AM, Andrew Voronkov wrote:
> >
> > > Dear Amber users, I have problems with binding energy calculation using
> > > binding_energy.mmpbsa. The snapshots seem to be extracted correctly
> > > with the appriopriate names (2770
> snapshots)."[voronkov.t60-2PM-CAP-1IJYCAP]$ $AMBERHOME/exe/
> > > mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log />
> > > /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o
> sander_com.1.out
> > > -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful
> />[voronkov.t60-2PM-CAP-1IJYCAP]$
> > > /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o
> sander_com.1.out
> > > -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful" />maybe
> I need to place these files sander_com.in -o
> > > sander_com.1.out locally, but I haven't found them in the tutorial?The
> > > log is in the bottom, but seems not to be very informative, probably
> some
> > > problems with files names or command flags order?Sincerely
> > > yours,Andrew=>> 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 =>
> > > ./1ijy-pmc_v.prmtop Found RECPT =>
> > > ./1ijy_v.prmtop Found LIGPT => ./pmc_v.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
> > > _______________________________________________
> > > 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 18 2010 - 04:00:05 PDT
