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

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Wed, 02 Jun 2010 17:15:56 +0400

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]$ $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful [voronkov.t60-2 PM-CAP-1IJYCAP]$ /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/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 > > > > > > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber -------- Завершение пересылаемого сообщения -------- 

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application/octet-stream attachment: binding_energy.mmpbsa

Received on Wed Jun 02 2010 - 06:30:07 PDT