Re: Re: Re: [AMBER] error - binding_energy.mmpbsa run from Jason Swails on 2010-06-02 (Amber Archive Jun 2010)

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 2 Jun 2010 09:20:52 -0400

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 <drugdesign.yandex.ru>

> Addtional data: sander_com.in file is listed below and
> binding_energy.mmpbsa is in the attachment. Sincerely yours,<br
> />Andrew File generated by mm_pbsa.pl. Using  MM GB<br
> /> &cntrl   ntf    =
> 1,       ntb    =
> 0,       dielc  = 1.0,  
> idecomp= 0,   igb    =
> 2,       saltcon= 0.00,   offset =
> 0.09,   intdiel= 1.0,     extdiel= 80.0,<br
> />  gbsa   = 0,       surften=
> 1.0,   cut    = 999.0,   nsnb  
> = 99999,   scnb   = 2.0,    
> scee   = 1.2,   imin   =
> 1,       maxcyc =
> 1,       ncyc   = 0,<br
> /> &end Sincerely yours, Andrew --------
> Пересылаемое сообщение -------- 18.05.10, 09:49, "Andrew
> Voronkov" <drugdesign.yandex.ru <lt%3Bdrugdesign.yandex.ru>>:<br
> /> 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.<br
> />The snapshots seem to be extracted correctly with the appriopriate names
> (2770 snapshots). "[voronkov.t60-2 PM-CAP-1IJYCAP]$
> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log<br
> /> /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o
> sander_com.1.out -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not
> successful [voronkov.t60-2 PM-CAP-1IJYCAP]$
> /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 "<br
> /> 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 <br
> />=>> Reading input parameters Found PREFIX => snapshot 
> Found PATH => ./ Found COMPLEX => 1 Found RECEPTOR =>
> 1 Found LIGAND => 1 Found COMPT => ./1ijy-pmc_v.prmtop<br
> /> 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<br
> /> 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<br
> /> 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<br
> /> 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<br
> />> > On Sun, May 16, 2010 at 6:53 AM, Andrew Voronkov wrote:<br
> />> > > 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]$ $AMBERHOME/exe/ > >
> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log /> <br
> />> > /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o
> sander_com.1.out > > -c ./snapshot_com.crd.1 -p
> ./1ijy-pmc_v.prmtop not successful />[voronkov.t60-2PM-CAP-1IJYCAP]$
> > > /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 > > _______________________________________________<br
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> > http://lists.ambermd.org/mailman/listinfo/amber > ><br
> />> > > > <br
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-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 02 2010 - 06:30:11 PDT