Re: [AMBER] error - binding_energy.mmpbsa run from Jason Swails on 2010-05-16 (Amber Archive May 2010)

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 16 May 2010 07:40:22 -0400

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 <drugdesign.yandex.ru>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]$ $AMBERHOME/exe/
> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log<br
> />       
> /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out
> -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful<br
> />[voronkov.t60-2PM-CAP-1IJYCAP]$        
> /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 "<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<br
> />    Presuming executables of amber suite to be in
> /home/osolodkin/amber10/exe =>> Reading input parameters<br
> />    Found PREFIX => snapshot    
> Found PATH => ./     Found COMPLEX => 1<br
> />    Found RECEPTOR => 1     Found
> LIGAND => 1     Found COMPT =>
> ./1ijy-pmc_v.prmtop     Found RECPT =>
> ./1ijy_v.prmtop     Found LIGPT => ./pmc_v.prmtop<br
> />    Found GC => 0     Found AS =>
> 0     Found DC => 0     Found MM
> => 1     Found GB => 1    
> Found PB => 1     Found MS => 1<br
> />    Found NM => 0     Found PROC
> => 2     Found REFE => 0    
> Found INDI => 1.0     Found EXDI => 80.0<br
> />    Found SCALE => 2     Found LINIT
> => 1000     Found PRBRAD => 1.4<br
> />    Found ISTRNG => 0.0     Found
> RADIOPT => 0     Found NPOPT => 1<br
> />    Found CAVITY_SURFTEN => 0.0072<br
> />    Found CAVITY_OFFSET => 0.00    
> Found SURFTEN => 0.0072     Found SURFOFF =>
> 0.00     Found DIELC => 1.0    
> Found IGB => 2     Found GBSA => 1<br
> />    Found SALTCON => 0.00     Found
> EXTDIEL => 80.0     Found INTDIEL => 1.0<br
> />    Found SURFTEN => 0.0072    
> Found SURFOFF => 0.00     Found PROBE => 0.0<br
> /> =>> 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<br
> />        Calc MM/GB/SAS 
> _______________________________________________
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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 Sun May 16 2010 - 05:00:03 PDT