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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Received on Sun Apr 16 2006 - 06:07:05 PDT
