Re: Re: [AMBER] error - binding_energy.mmpbsa run

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Tue, 18 May 2010 09:49:27 +0400

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" <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
> >
> >
>
>

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Received on Mon May 17 2010 - 23:00:03 PDT
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