AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA not successful

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Fri Aug 14 2009 - 20:20:55 CDT

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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