AMBER Archive (2006)

Subject: AMBER: molsurf.c error

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Thu May 04 2006 - 11:00:31 CDT


Hi all,

I am still with problems with mm_pbsa calculations. The error is the
following:

-- > MAXAT=10000 exceeded
molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
Use of uninitialized value in multiplication (*) at
/scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
Use of uninitialized value in multiplication (*) at
/scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
Use of uninitialized value in multiplication (*) at
/scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
    No data for 0+0 MS SURF 0

[1] Exit 134 mm_pbsa.pl mm.pbsa.in > mm.pbsa.out

As I previously increased the variable MAXAT in molsurf.c file (as said in
http://structbio.vanderbilt.edu/archives/amber-archive/2004/1336.php), I
don´t understand the reason of this error. Should I change the MAXAT
variable in another file?
Does anyone know what the error with molsurf.c:1055 means and how to solve
this problem?
I think my input files are ok. I created pdb files from the unsolvated top
files and they look normal.
Here is mm_pbsa.out:

=>> Init data
    Presuming executables of amber suite to be in /scratch/amber8/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 => 0
    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
        Generate PQR
        Calc MS
    Calc contrib for ./complex _rec.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        Calc MS
    Calc contrib for ./complex _lig.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        Calc MS

=>> Doing statistics
=>> Values of global variables
    TEMP = 300
    R = 8.314
    gammaP = 0.005
    betaP = 0.0
    gammaG = 0.0072
    betaG = 0
=>> Reading input
=>> Reordering files
    Final order:
    1. complex _com.all.out: -
    2. complex _rec.all.out: -
    3. complex _lig.all.out: -
=>> Reading files
    Reading complex _com.all.out
    WARNING: Missing SURF for MS in 0 -> Taken from -1
    Reading complex _rec.all.out
    Checking CALC
    WARNING: Missing SURF for MS in 0 -> Taken from -1
    Reading complex _lig.all.out
    Checking CALC
    WARNING: Missing SURF for MS in 0 -> Taken from -1
=>> Treat special parameters
=>> Calc missing parameters
    Processing MM GAS
        Doing 1 MM ELE
    No values for MM_ELE existing -> Skipping
    Processing MM INT
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
    Processing MM ELE
        Doing 1 MM ELENB
        Doing 1 MM ELE14
        Doing 1 MM ELENB
        Doing 1 MM ELE14
        Doing 1 MM ELENB
        Doing 1 MM ELE14
    Processing MM VDW
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
    Processing PB PBSOL
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
    Processing PB PBELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
    Processing PB PBTOT
        Doing 1 PB PBSOL
        Doing 1 MM GAS
    No values for MM_GAS existing -> Skipping
    Processing MM GAS
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
    Processing PB PBTOT
        Doing 1 PB PBSOL
        Doing 1 MM GAS
        Doing 1 PB PBSOL
        Doing 1 MM GAS
        Doing 1 PB PBSOL
        Doing 1 MM GAS
=>> Calc delta from raw data

Thanks in advance!
Miguel

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