AMBER Archive (2007)

Subject: AMBER: Error in MMPBSA Calculation

From: msubhamoy_at_ibab.ac.in
Date: Tue Aug 21 2007 - 00:53:17 CDT


Respected Sir
I have tried a lot. but my mmpbsa program is stopping here. There is no problem
with the receptor file.
I have checked. Please help me out .

                                                        S.mukherjee

=>> Init data
    Presuming executables of amber suite to be in /home/gsmith/amber9/amber9/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH => ./
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./comp_nowat.prmtop
    Found RECPT => ./rec.prmtop
    Found LIGPT => ./lig.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
                                                                                                          24,5

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
        Generate PQR
        Calc MS
    Calc contrib for ./snapshot_com.crd.2
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        Calc MS
    Calc contrib for ./snapshot_com.crd.3
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
........ it continued till
 Calc contrib for ./snapshot_com.crd.4830
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        Calc MS
 then it gave

 Calc contrib for ./snapshot_rec.crd.1
        Calc MM/GB/SAS
there is no problem with the receptor file..... then why is the program stopping?

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