The error is not very obvious here (as you have noticed). sander_com.in and
sander_com.1.out are files created by mm_pbsa.pl, so you do not need to do
anything with these files. These files are created by the script and then
used by the script. You mentioned that the coordinates appear to have been
made correctly, but have you visualized (in VMD, PyMol, etc) them (receptor,
ligand, and complex for a few different snapshots) to make sure they are
what they are supposed to be? Sander could have failed because the
coordinate file did not match the corresponding prmtop. Also, if you open up
and read sander_com.1.out, it should have a much more informative error
(hopefully), since this is a sander mdout file and should have applicable
error files. Take a look at these things and see if they help you pinpoint
the exact error.
Good luck!
-Bill
2010/6/3 Andrew Voronkov <drugdesign.yandex.ru>
> Here is the text without markup., should be possible to read now.
>
> Addtional data: sander_com.in file is listed below and
> binding_energy.mmpbsa is in the attachment.
>
> Sincerely yours,
> Andrew
>
> File generated by mm_pbsa.pl. Using MM GB
> &cntrl
> ntf = 1, ntb = 0, dielc = 1.0,
> idecomp= 0,
> igb = 2, saltcon= 0.00,
> offset = 0.09,
> intdiel= 1.0, extdiel= 80.0,
> gbsa = 0, surften= 1.0,
> cut = 999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
> imin = 1, maxcyc = 1, ncyc = 0,
> &end
>
> Sincerely yours,
> Andrew
>
> -------- Пересылаемое сообщение --------
>
> 18.05.10, 09:49, "Andrew Voronkov" <drugdesign.yandex.ru>:
>
>
> 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" :
>
> > 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
> > >
> > >
> >
> >
>
> 02.06.10, 17:20, "Jason Swails" <jason.swails.gmail.com>:
>
> > Hello,
> >
> > Please try re-sending the email without all of the markup. I couldn't
> read
> > any of that.
> >
> > Thanks!
> > Jason
> >
> > 2010/6/2 Andrew Voronkov
> >
> > > Addtional data: sander_com.in file is listed below and
> > > binding_energy.mmpbsa is in the attachment.Sincerely yours,
> />AndrewFile generated by mm_pbsa.pl. Using MM GB /> &cntrl ntf =
> > > 1, ntb =
> > > 0, dielc = 1.0,
> > > idecomp= 0, igb =
> > > 2, saltcon= 0.00, offset =
> > > 0.09, intdiel= 1.0, extdiel= 80.0, /> gbsa = 0, surften=
> > > 1.0, cut = 999.0, nsnb
> > > = 99999, scnb = 2.0,
> > > scee = 1.2, imin =
> > > 1, maxcyc =
> > > 1, ncyc = 0, /> &endSincerely yours,Andrew--------
> > > Пересылаемое сообщение --------18.05.10, 09:49, "Andrew
> > > Voronkov" : />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]$
> > > $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
> /> /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o
> > > sander_com.1.out -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not
> > > successful[voronkov.t60-2 PM-CAP-1IJYCAP]$
> > > /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/SAS16.05.10, 15:40, "Jason Swails" :>
> > > 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.orghttp://lists.ambermd.org/mailman/listinfo/amber/>-------- Завершение пересылаемого сообщения -------- />
> > > _______________________________________________
> > > 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 03 2010 - 05:00:04 PDT
