AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA not successful

From: Jordan Monnet (monnet.jordan_at_free.fr)
Date: Fri Aug 14 2009 - 19:05:00 CDT

Hello,

What does pbsa_com.1.out say?

--jordan

* workalemahu berhanu (wgberhanu_at_gmail.com) wrote:
> Dear Amber users
>
> I am not getting the results for mmpbsa calculation Calculate the
> binding free energy. Can anyone help me?
> I have
> given both my input and output files.
> This is my input
> @GENERAL
> PREFIX snapshot
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./GNNQQNYMYRSB.prmtop
> RECPT ./GNNQQNYSB.prmtop
> LIGPT ./MYR.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 2
> PB 1
> MS 1
> NM 0
> @PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> SURFTEN 0.0072
> SURFOFF 0.00
> @MM
> DIELC 1.0
> @GB
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> SURFTEN 0.0072
> SURFOFF 0.00
> @MS
> PROBE 0.0
> @PROGRAMS
> This is my Out put
> =>> Init data
> Presuming executables of amber suite to be in /u0/z/zz217/USG/amber/9.0/exe
>
> =>> Reading input parameters
> Found PREFIX => snapshot
> Found PATH => ./
> Found COMPLEX => 1
> Found RECEPTOR => 1
> Found LIGAND => 1
> Found COMPT => ./GNNQQNYMYRSB.prmtop
> Found RECPT => ./GNNQQNYSB.prmtop
> Found LIGPT => ./MYR.prmtop
> Found GC => 0
> Found AS => 0
> Found DC => 0
> Found MM => 1
> Found GB => 2
> 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
> 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
> Generate PDB
> Center PDB
> Calc PBSA
> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
> /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in -o
> pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop not
> successful
>
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    }><(({*>
__/

Jordan MONNET
Bachelor in Biology & Computer science
University of Paris Diderot (Paris VII)

http://monnet.jordan.free.fr/

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