AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA not successful

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Fri Aug 14 2009 - 21:43:23 CDT

Dear Sir,

If so, I think you should check the other output files to find some clues about the error. or you can show us those output files.
Good luck!

Qinghua

________________________________
From: workalemahu berhanu <wgberhanu_at_gmail.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Saturday, August 15, 2009 10:36:39 AM
Subject: Re: [AMBER] MM_PBSA not successful

Dear Qinghua

Hi
I introduced a line with fillratio=3.0 or 4.0 in the file pbsa.in. As
you explained in the mail archive
(http://archive.ambermd.org/200905/0326.html). The problem is still
there

mikre_at_nid00235:~/PRION/MMPBSA> 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

GNNQQNYMYRSB is the complex

Thank you

On Fri, Aug 14, 2009 at 9:20 PM, Qinghua Liao<fantasticqhl_at_yahoo.com> wrote:
> Hi,
>
> Maybe you should change the value of fillratio from default 2.0 to 3.0 or 4.0, you can have a try.
>
> Good luck!
>
> Qinghua
>
>
>
>
> ________________________________
> From: workalemahu berhanu <wgberhanu_at_gmail.com>
> To: AMBER_at_ambermd.org
> Sent: Saturday, August 15, 2009 5:45:41 AM
> Subject: [AMBER] MM_PBSA not successful
>
> 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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>
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