AMBER Archive (2006)

Subject: AMBER: MM-PBSA problem

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Fri Apr 14 2006 - 10:27:43 CDT


Hi, all,

I am trying to perform MM-PBSA calculations on a protein-ligand complex to
estimate the binding free energy. The complex is large (15504 atoms) and so
I needed to increase the variable MAXAT. However I am still having problems.
The calculation does not come to the end.
Here is my mm_pbsa.out:

    =>> Init data
    Presuming executables of amber suite to be in
/scratch/programs/amber8/amber8_mod//exe

=>> Reading input parameters
    Found PREFIX => complex
    Found PATH => ./
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./complex.top
    Found RECPT => ./protein.top
    Found LIGPT => ./ligand.top
    Found GC => 1
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 0
    Found PB => 1
    Found MS => 1
    Found NM => 0
    Found PROC => 1
    Found REFE => 0
    Found INDI => 1.0
    Found EXDI => 80.0
    Found SCALE => 2.5
    Found LINIT => 1000
    Found MAXC => 0.001
    Found PRBRAD => 1.4
    Found FOCUS => 0
    Found PERFIL => 80.0
    Found CHARGE => ./complex.crg
    Found SIZE => ./my_parse_delphi.siz
    Found SURFTEN => 0.00542
    Found SURFOFF => 0.92
    Found DIELC => 1.0
    Found PROBE => 0.0
    Found BOX => NO
    Found NTOTAL => 15504
    Found NSTART => 0
    Found NSTOP => 1
    Found NFREQ => 1
    Found NUMBER_LIG_GROUPS => 4
    Found LSTART => 15041
    Found LSTOP => 15156
    Found LSTART => 15157
    Found LSTOP => 15272
    Found LSTART => 15273
    Found LSTOP => 15388
    Found LSTART => 15389
    Found LSTOP => 15504
    Found NUMBER_REC_GROUPS => 4
    Found RSTART => 1
    Found RSTOP => 3760
    Found RSTART => 3761
    Found RSTOP => 7520
    Found RSTART => 7521
    Found RSTOP => 11280
    Found RSTART => 11281
    Found RSTOP => 15040
    Found TRAJECTORY => ./complex.trj
    Found DELPHI => /home/delphi/bin/delphi

=>> Checking sanity
    Checking GENERAL
    Checking GC
    Checking TRAJ
    Checking MM
    Checking PB
    Checking MS

=>> Creating input
    Sander input
    Delphi input
    make_crd input

=>> Creating coordinates
    Executing makecrd

Amber8 Module: make_crg_hg

usage: make_crd_hg < trajectory_file

=>> Calculating energy / entropy contributions
    Calc contrib for ./complex_com.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc delphi
            Run 0 0

To see if the problem was with Delphi, I try to use the PB method
implemented in the pbsa program, but it also gives error:

-- > /scratch/programs/amber8/amber8_mod//exe/pbsa -O -i pbsa.in -o
pbsa_com.1.out -c ./complexo-modelado_com.crd.1 -p
./complexo-finalsolv_oct_semsolv.top not successful

[1] Exit 25 mm_pbsa.pl mm.exp2.in > mm.exp2.out

The pbsa_com.1.out end with the following error:

======== PB Initialization ========

     Max PBMD Nonbonded Pairs: 7136003 3767472

PB bomb in pb_aaradi(): ZERO sigma found for non-hydrogen atom

The content of the mm_pbsa.out is:

=>> Init data
    Presuming executables of amber suite to be in
/scratch/programs/amber8/amber8_mod//exe

=>> Reading input parameters
    Found PREFIX => complex
    Found PATH => ./
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./complex.top
    Found RECPT => ./protein.top
    Found LIGPT => ./ligand.top
    Found GC => 1
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 0
    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 => 2.5
    Found LINIT => 1000
    Found MAXC => 0.001
    Found PRBRAD => 1.4
    Found RADIOPT => 1
    Found FOCUS => 0
    Found PERFIL => 80.0
    Found CHARGE => ./complex.crg
    Found SIZE => ./my_parse_delphi.siz
    Found SURFTEN => 0.005
    Found SURFOFF => 0.0
    Found DIELC => 1.0
    Found PROBE => 0.0
    Found BOX => NO
    Found NTOTAL => 15504
    Found NSTART => 0
    Found NSTOP => 1
    Found NFREQ => 1
    Found NUMBER_LIG_GROUPS => 4
    Found LSTART => 15041
    Found LSTOP => 15156
    Found LSTART => 15157
    Found LSTOP => 15272
    Found LSTART => 15273
    Found LSTOP => 15388
    Found LSTART => 15389
    Found LSTOP => 15504
    Found NUMBER_REC_GROUPS => 4
    Found RSTART => 1
    Found RSTOP => 3760
    Found RSTART => 3761
    Found RSTOP => 7520
    Found RSTART => 7521
    Found RSTOP => 11280
    Found RSTART => 11281
    Found RSTOP => 15040
    Found TRAJECTORY => ./complex.trj

=>> Checking sanity
    Checking GENERAL
    Checking GC
    Checking TRAJ
    Checking MM
    Checking PB
    Checking MS

=>> Creating input
    Sander input
    PBSA input
    make_crd input

=>> Creating coordinates
    Executing makecrd

Amber8 Module: make_crg_hg

usage: make_crd_hg < trajectory_file

=>> Calculating energy / entropy contributions
    Calc contrib for ./complex _com.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA

Does anyone know what may be happening? Is there something wrong with the
parameters I am using?

Thanks in advance

Tetrass

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